That's a strange one, any chance of a screen shot so i can take a look at problem?
EVE doesn't touch ballistic effects.
Better Smoke and Ballistics includes some optional versions, is it possible you installed the realistic version? because that pretty much removes muzzle flashes completely.
Check in your data folder and see if there's any files under Meshes\Effects\MuzzleFlashes\
if there is, try to find out what mod they came from. if you can't find out just delete them and the game will load the original files from the BSA.
I hope this helps.