Need an answer

Two weeks ago I completed my antibiotic regiment for H Pylori.  I am still on the Carafate and the Nexium.  The gnawing and empty feeling in my stomach still continues.  I saw my doctor on Monday again, and she says it takes a while to get this bacteria out of my system.  I am really not feeling very much improved, especially when I wake up in the night with this miserable feeling.  There are days I feel that I am getting better, then I seem to be back to square one again.  Does it make sense that the ulcer is still there, and is healing even thought the bacteria have been killed?  And is this why I am feeling this way?