Reclipsen causing stomach pains after taking pill. Ppi helps some, but still getting daily indigestion. Will this subside? 5 weeks on reclipsen.

Try another pill. If you are truly not tolerating a birth control pill after an entire cycle (and needing to take another pill to counteract a side effect), then it sounds like you and that pill are not a good match. Omeprazole is an antacid designed to be taken in 2 week bursts and is not really meant to be taken for long periods to counter a side-effect. I think it would be worth discussing changing pills.
Maybe. Have you tried taking the pill with food, or at night? If you do so and it still causes stomach upset after a two-month trial, follow up with your doc and try another brand. You should not need to take a to ach medicine to tolerate your birth control pill.