What time of day do you give the omeprazole and how much does he have? If it's in one dose in the morning it could be that by the end of the day it's starting to wear off and he is comfort feeding during the evening/ night, babies metabolise PPI's faster than adults so they sometimes need to have their dose split into 2, but that depends on how much he is having.
The other thing you can do is to give the omep in the evening rather than the morning if you aren't already.
Laura