MShall,
If your regular bowel habits have changed since taking the new Rx prescribed by your doctor then you need to call your doctor to discuss the troubling 'side effects' you are experiencing. The Rx he/she gave you may not be quite right for you and they can consider other options for you. But, if you don't call to talk to them they can't know you are experiencing problems.
Put a call in to them today.
Hope you're feeling better soon,
Elizabeth