Reflux peaks between 4-6months and I am wondering if it is bothering her in the night. I would certainly give the omeprazole a bit longer to take effect. (It can take up to 2 weeks) and see if she improves.
Can you post her EAS
When you say she wakes a lot, how is she waking, and how frequently. ie are they all in a 4-5 hr period every 45mins oo more spaced...and does she wake crying, screaming, talking...
(HUGS)