Hi and welcome to Discuss Cooking
Canning safely is an exact science. It's not a good idea to make changes to a recipe until you understand thoroughly what can safely be changed and what can't.
With water-bath canning, you have to make sure the pH of the solution is less than 4.6. Adding a low-acid ingredient like jalapeños will increase the pH of the mixture and it might not be safe anymore. Also certain thickeners, like flour and cornstarch, are not safe for canning. I suggest you make adjustments as you open the jars.
Btw, did you use a safe, tested recipe? There are a lot of random people on the internet publishing recipes that may or may not be safe. I can give you a few safe sites if you want.