I would toss it. Tomatoe sauces are the one thing I have had turn on me.

The most probable cause of the discolored tomatoes was due to too much headspace in the jar since you didn't have this problem with other jars from the same batch. Discolored food doesn't always mean it's spoiled or unsafe to eat, but unfortunately it CAN indicate bacteria growth just as well. Sometimes there are chemical reactions with the minerals in hard water that can cause discoloration. I've seen the seeds in tomatoes turn dark because of the enzymes in the seeds reacting with high iron content in the tap water.

So if you decide to use it, be sure to inspect it carefully as you open the jar. Unfortunately, the food can look, smell, and taste normal and STILL be contaminated with bacteria. Here are some things to look for.

(Source: http://canninginfowarehouse.com/Canner-Problems.html)
How Do I Recognize if My Food Has Spoiled?

You will want to examine each jar very carefully prior to using it. First check to see that the vacuum seal is present. Do not use any food product that shows signs of having spoiled or if the lid is unsealed. Spoilage produces gasses that cause the lids to swell and/or break the seal. Canned food that is sealed with a lid that does not require a can opener to pry it off must not be used. Also, visually examine your jars for other signs of spoilage which could be present.

Signs of possible Spoiled Food:

*Broken Seals
*Seepage
*Mold
*Yeast Growth
*Gassiness
*Fermentation
*Cloudiness
*Slime
*Spurting Liquid
*Disagreeable Odors

Your home canned foods that are showing signs of being spoiled need to be disposed of in a way that no person or animal will come into contact with the food. Canning jars that are suspected of containing spoiled low-acid or tomato products have to be handled very carefully. Spoiled vegetables, meats, poultry, seafoods, and tomato products must be detoxified to prevent any possible contamination from botulism that could be present. To detoxify the food, jar, lid, and band, place all of the items into a deep pot. It is not necessary to remove the food from the jar. Carefully cover all items with 1 to 2 inches of water. Cover the pot. Bring the water to a boil and boil for 30 minutes. Be careful not to splash water or food outside of the pot. Allow the contents of the pot to cool. Discard all of the contents of the pot.

To clean the surfaces that came into contact with the suspect food you will need to use a solution of chlorine bleach and water (1 part chlorine bleach to 5 parts water). Allow the cleaning solution to stand for 5 minutes before rinsing. Dispose of sponges, hand towels, and dishcloths that were used in the detoxifying process.

Yeah, I think I'm going to just toss it.. it might be ok, but I'm just too leery about it.

And heh, didn't even think about the fact that it could by my hard water/iron in the water that could be the culprit, but maybe- since it seems to have been the last jar it might also be the jar with the most seeds too, that might make as much sense as the overly much headroom causing the problem.

I didn't realize there is a process to this though, thanks Grainlady! When I have the time next week to properly dispose of it, I will do so.

I would also think that the additional headroom would be a factor. It had more air and if it doesn't all get expelled, the air can lead to both oxidation and bacteria growth. If we have a jar that doesn''t get full, we always use that one first -- may not even process it -- just straight to the fridge, depending on what it is.