the chemical combiner recipe for apples appears to make spruce logs instead of apples

Please use the transfer recipe functionality in JEI (the [+] button) while you have the Chemical Combiner GUI open to lock the recipe to apples, which will prevent this from happening. Please let me know if you continue to have trouble or can't figure out what i'm referring to.

Actually, here, I recorded a quick demonstration for you

Video

Please comment if you are still having issues