Salsa morning after taste
It could be the allithiolanes in the onions (and to some extent, garlic) at work. You can't smell them, really, but they come out of chopped onions gradually and have a very acrid / bitter taste.
There's no way to eliminate it 100% except for cooking, as far as I know, but you can peel and halve your onion and soak them in clean cold water with a bit of acid added (lemon or lime juice) for about 20 minutes before you use them. This should lessen the extent that you notice the taste. Alternatively, or additionally, you could use shallots or other smaller, milder red onions which don't have as much of a problem with it.
It comes out in that sort of &quot;milky&quot; liquid that you see when you cut open most white onions.
Commercial salsa gets rid of it through the manufacturing process.