Can you send the pics to:
rocketman1022000@yahoo.com

With the title "trouble with my indoor tomato/jalapeno grow"

PH is fine. Keep temp below 65f.
This is what you need.
BROWN ROOTS-Do you use a "cleaner" what nutrients do you use? Get to your local hydro store and ask the person there about a "cleaner" and the generial hydroponic line. H202 can work good. empty your water then add new water. add H202 at the right ammount(you can find out online) let it run for 30 mins then add your nutes. Cleners kill off bad algae and other mold on the water. the blotchs on your leaves are most likely from your roots as most problems are. I see you use flora well go get flora shield!!!

So there you go. The answer to your problem is florashield.

I would want to see some pictures first. Brown roots aren't always a problem. Roots tend to discolor the older they get anyway, and the nutrients themselves can stain/tint the roots also. Nether is a problem, and natural. I'm more concerned with the statement:

"the first thing I notice was small irregulare light blotches on the bottom tomatoe leaves as well as a greyish patern on the same leave but on the jalapeno leaves."

That sounds like a mildew (fungus), like powdery mildew that starts as small dusty white or light gray spots, and grow together into a continues mat of fungus that resembles something like talcum powder on the plant. Mildew/fungus will also affect the overall health of the plant, and tomatoes are very susceptible to fungus problems. But again I would like to see some pictures before I assume there is a fungus problem. I would also like to know what the humidity level is/was. Powdery mildew thrives in dry climates, but needs damp spots, or areas of high humidity to germinate the spores first. Where Downy Mildew is probably more likely in wet climate, and/or high humidity situations, and look similar.

Yes good point. If you have high humidity that could be a prob.

Like HH, I would like to see pics. Can you link them? Or just google how to post pics on here. I always have to do that as I forget every time.

I think we are missing info. What kind of water are you starting with? What nutes, exactly? What you are describing seems to me to be a lockout issue. The brown on the roots is often due to fall out of minerals. Maybe rusting iron? Ever seen all the rust on a bathroom wall of old homes where the iron in the mist collects on the wall? This is even worse in high pH water. Iron falls out faster and faster as you go above 7. The pH of your solution may be at 6, but that doesn't mean it's staying there when collected on the roots as the roots change the pH. As suggested, use a cleaner to remove the deposits.

Anyway, from the little info available, I'd hazard a guess at nute deficiency in the plant. Not necessarily in the solution. Often times, nute deficiency is a matter of uptake rather than content. So, don't go straight to adding nutes. The leaf curl can be a calcium deficiency or an over abundance of nitrogen or even both. Calcium helps make the cells strong. Nitrogen increases growth speed. Sometimes it happens faster than all the cells can handle and you get distortion in the leaves. Very common in peppers as people tend to over fertilize them. Especially if they put them in the same system as tomatoes. They have very different needs. Hard to say if this is happening without seeing the plants in a good, true color pic (no adjustments due to flash or backlight compensation). The spots can be a magnesium or calcium deficiency. Others, too, but these are common ones. Again, need to see the plants.

Again without seeing any pictures, it's really hard to come to any conclusions. But here a few links with symptoms and pictures of powdery, and downy mildew. The symptoms sound more similar to the downy mildew to me, with both the curling leaves, and spots on the leaves. But powdery mildew also causes pour plant health as well.

Downy Mildew
Quote taken from the above link:

"Symptoms
Symptoms can be confused with other plant problems. Leaves may become mottled and yellowed, resembling nutritional deficiencies. On some plants, downy mildew infection may look similar to injury from foliar nematodes. In both cases, angular lesions are bounded by leaf veins. However, downy mildew infection results in a soft, fluffy gray, brown or purple fungal sporulation developing on the underside of leaves. On coreopsis, the fungal sporulation is white.

Symptoms can also vary depending upon the host plant. On snapdragons, infected plants are yellow and stunted. You may see downward leaf curling on the young seedlings. On salvia, angular yellow blotches can be seen between the leaf veins. On pansy, leaves turn mottled and off-color with purple blotches. Pale green or yellow patches develop on geum. Purplish patches occur on lamium and veronica. On roses, leaves develop angular dark purple to black areas and may turn yellow and drop."

Some more links with symptoms and pictures
Downy mildew on grapevines
DOWNY MILDEW IN BASIL
Powdery mildew
Powdery Mildew Quick Facts

Easy to tell if it's either of the mildews: Are the spots fuzzy or look like they have powder sugar on them? They will if it's either of those. I doubt it's the problem, though.

First, the original post doesn't mention fuzz/powder and I have a feeling it would have. Of course, it could have been an oversight.

Second, neither of these are particularly known for tomato and peppers indoors. Sometimes in a greenhouse, but that's due to the spores being carried in on the wind and through the vent system and the humidity in a greenhouse make ideal conditions for spore adherence. Plus, it's really too early for mildew spores in KS. There hasn't been enough outside foliage to propagate them, which means they also aren't likely to have been carried in from outside. Give it another couple weeks, though.

Third, neither cause brown roots, but some things that cause brown roots do cause the symptoms described. So, if it's either of the mildews mentioned, that's independent of the brown roots. The brown roots could (though not necessarily) be an indicator of a nute issue whether you have the mildew problem or not.

Ya, I agree. That's why I would have liked to see some pictures. But in case the original poster couldn't post them, I wanted to post some links to descriptions and pics so they could see if that seems like what they are experiencing. Also as you mentioned regardless, that doesn't mean there is only one issue they are dealing with or not. But I'm guessing that at the time of the original post when noticing the irregular light blotches, as well as the grayish spots, simply noticing if they were a fuzzy or dusty substance was as you mentioned, just an oversight or missing information. And the light blotches wouldn't necessarily need to be fuzzy or dusty for the downy mildew on the tops of the leaves (where I think they were noticed), so assuming they are on the tops of the leaves, and the fungus is on the bottom of the leaves, it sure seems to fit the situation.

Even though the fungus needs to be growing to propagate the spores, the spores will only need air current to travel, and the spores are seeds that will survive winters. Once they make it into a greenhouse, it's not winter for the spores anymore, and will germinate anytime conditions are favorable. The downy mildew even prefers "cool" moist conditions, and can also cause the leaf curl (that's being experienced).

But the reason that I don't really focus on the statement about the brown roots is mainly because there are brown roots, and then there are brown roots. Everyone's idea of what's brown is, is different. Basically there are many shades of brown, and the original posters statement was "the roots are getting a brownish tint." To me that suggests that they seem to be going form a solid and/or bright white that they are used to seeing, to a slight off-color (brownish).

And as I mentioned, older roots tend get a brown tint anyway. The poster never said how old the plants were that I remember, and I assume they are not exactly young plants. Also some nutrients will naturally give the roots a brownish tint as well, even if so. So without any more information or pictures to go on, I simply don't see the statement of the roots getting a brownish tint as a problem or issue at this point. But that's not to say it isn't the first visible sign of a problem, or even to say that there isn't another issue going on as well.

oops. sorry guys for the delay on the post. I have been searching my ass off! I figured out the prob. I belive it is a combonation of powdery mildew as well as a root rot problem. But i dont think the roots are too awful bad. I went back to the hydro store and picked up some hydrozome. I have been emptying my res and scrubbing with alcohol(Ive been told H202 kills ALL bacteria. she said you need some GOOD bacteria for the plant to do good). After that i run flora kleen through for a few hours. when i topped back up I put low lewel amounts of Hydrozome as well as- belive it or not! Superthrive-I figured it could help with stress. just 1 drop a gallon! After trimming the worst roots I hit the leaves with sulfer for the Mildew and, voila!!! It seems to be dooing great. it is back to rapid growth already. 2 weeks of that is all it took. The roots that looked best are growing feeder hairs like crazy! I plan on continueing this regimine for a while to make sure no rot is continuing. Oh yeah, I also increased the slope of my trough as well as added extra air stones.
Thanks for the help!!!