I am on an older version of AC, and discovered a similar problem.
Medications renewed based on pharmacy requests did not populate accurately to my med list.
Since then, I have not renewed medications from the pharmacy request/refill screen.
Instead, I go to my med list and renew meds from that.
I then go back to the request/refill screen and deny the meds on the refill requests, indicating that i did so already.
I have found that it leaves me with a more reliable med list.
I plan to continue doing that until sometime after I upgrade to a newer version of AC.
Hope that helps.
ACZ