Yes, unfortunately, one of the problematic side effects of taking that kind of medication over time is the possibility of stomach damage. And with that often goes the possibility of nutrient malabsorption, which is certainly not going to help any other conditions you have.
This may be the time to consider supplementing with certain vitamins and minerals. Some essential fatty acids from fish oil to help the mucosal membranes of your gastric tract, and some of the B-vitmains, perhaps.
We have a lot of info on this sort of thing over at the Vitamin and Mineral forum:
http://neurotalk.psychcentral.com/forum49.html