Water baths don't usually siphon out. That occurs when you pressure can and release the pressure or cool down too quickly. Chopped tomatoes may have had some air space between the bits when filling the jars. If they were a cold pack, they would shrink some once heated. I presume that you also added the necessary citric acid or bottled lemon juice? The jars, in a boiling water bath should have water about 2 inches above the tops of the jars, and you leave the cover on the canner when processing.

It depends. By chopped what do you mean exactly ? Did you add any liquid to the jars ? If you just packed them in raw, no added liquid, then they are not processed long enough. You must be sure you are using the right time for the type of pack.
The 40 min. pints/45 min. is for those packed with WATER added to each jar . Plain tomatoes in a jar, packed without the water takes 85 min. If you did not add the water, then you need to either reprocess within 24 hours of the initial canning or put in the fridge and eat within a couple days or pop the seals and freeze the jars.
They are not safe to reprocess after the 24 hours. So, your have been canned too long, and sorry, but you should throw them away if you did not add the water to the jars. If you did and the headspace is down, you can use them.
The bottled lemon juice or citric acid crystals must be added, too, as was said. Even in pressure canned tomatoes the added acid is necessary.
You probably did a raw pack, right ? They will mush down and that is what you will get,a lot of shrinkage. It isn't necessarily siphoning if you used a raw pack. A hot pack will really help with tomatoes. Also, if you did not leave the jars in the canner for an additional 5 min. after processing and removing the lid, that can also cause siphoning.
It is very important for the water to be over the jars, too, as Ken said.

Here is a link to the current instructions for safely canning tomatoes. It provides instructions for several different methods and the processing time needed for each.

I agree with Linda Lou, we need to know exactly which recipe and method you used for the canning and the processing to determine if they are safe or not.

If you used the Step-by-Step picture instructions in the BBB, pre-cooked them for the hot pack, and added the boiling water as required then the most likely explanation is that all the air was not removed from the jars first or they weren't heated enough first.

If you added the required acid they are probably safe but if it has been less than 24 hours since they were done we can explain how to re-process them if you wish.

Dave

Here is a link that might be useful: NCHFP - How to can tomatoes

Thanks for your help everyone! I put the chopped tomatoes (I cut the tomatoes into chunks) in warmed jars and then filled it with hot water and lemon juice. I used 2 tablespoons for the quart jars and 1 tablespoon for the pints. I also ran a butter knife through it to release any bubbles that may have been trapped.

I did leave the cover on during processing, but removed the jars right away instead of leaving them in the canner. I have another laundry basket of tomatoes ready for canning so, this time, I'll see if leaving them in the canner solves my problem!

I had this happen last fall--my jars had an inch or two of head space per quart after processing. I purchased a late harvest case of ripe tomatoes and did raw pack without water, and processed for the 85 mins or so. I think the tomatoes themselves were not very juicy or were full of air, so the air released from the fruit as it cooked in the jars, causing the space. We just ate the last jar a month or so ago.

I made the crushed tomatoes recipe (with no added liquid)last night from NCHFP, and am very happy with the results. I think the 5 minute cook time in the pot and then a shorter time in the BWB makes for a firmer product (than the raw pack/long processing time), despite being crushed.
Carrie

Here is a link that might be useful: Crushed Tomatoes with no added liquid.

I agree, the crushed tomatoes are the best in my opinion.
Please, do not use a metal knife in the jars. The metal weakens the glass, even though you don't see the scratches. The glass can break from being weakened if you keep using the metal. Use a thin plastic knife, a spatula, or a chop stick instead. You can buy a special bubble freer wand, too.

humblegyrl, I've had that happen to some extent when I raw pack tomatoes, I only suppose it is shrinkage or that I have air trapped in the tomatoes that I haven't been able to expel. One of the reasons I don't rawpack them any more.

I hotpack the tomatoes, because they are "prettier" too, LOL. They don't tend to float or separate as much and I don't get the shrinkage that I do with a raw pack. I don't care for the lemon juice flavor and my mother is allergic to lemons, so I add the citric acid.

Thanks, Linda Lou, a chopstick is a good idea. I broke my thin plastic scraper by shutting it in the drawer a couple of days ago and have been trying to think what else I could use.

Annie

It is so scary to think how things have changed for canning. My mother never even did a boiling water bath for her tomatoes. She did what she called a boiling pack. Just packed boiling tomatoes into jars and put on the lids. She at least sterilized everything before, but the jars weren't even processed after. YIKES! Some of those tomatoes were still in the basement when we cleaned out after my Dad died this spring. I am glad I have learned more and knew how unsafe they were. Down right scary! Have things changed! For the better, for sure.

yikes gardensewer I think that is STILL how my aunts do things...makes me afraid to eat there now!

Well, my BIL open kettle "cans" salsa and that's even worse. So are the green beans with vinegar my cousin processes in her little steam canner. (I don't mean pickled green beans; I mean an old recipe for fresh green beans with a couple tablespoons of vinegar.) Fortunately, unlike the salsa, the green beans never get cooked less than 30 minutes before serving so risk is minimal.

Carol