I've been having a terrible time this past month. I got hit with pouchitis late June and took a round of Biaxin. Thought I was doing OK but then got dehydrated. Went to ER for fluids. Was ok, finished antibiotics and felt good for about 2 weeks and then got hit again with pouchitis. This time the doctor put me on Levofloxacin. I was taking it for about 4 days and then got hit with severe cramps in all different muscles in my body. My hands would cramp around bottles I was trying to open, I would go up stairs and my legs would cramp into rigid limbs. It was horrible. I would sneeze and my stomach and back muscles would seize up. You get the picture. It was bad- and I was dehydrating again! I went to the ER- They gave me 3 bags of fluid, did a full blood panel and the only thing that showed was out of wack was Magnesium. So, they gave me 2 pills of that and sent me home. Well, I get home and within 2 hours I feel like I am going to vomit the nothing that is in my stomach. I kept dry heaving. All through the night. I finally took a phenergan and it subsided. Does anyone out there think that my antibiotics might be eating away the good bacteria that is inside my stomach? I constantly feel like I'm going to faint or vomit. I know these are the side effects of the antibiotics but what happens if it continues when I get off the antibiotics- in 3 days. Now today I have harsh stomach cramping. I just feel like crying.
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Sounds like a reaction/intolerance to the antibiotic and should resolve shortly after stopping the antibiotic. It is possible to develop a C. difficile infection due to antibiotic use, and that would cause serious diarrhea, cramping, gas, bloating, bleeding, etc. that would NOT necessarily go away after stopping the antibiotic.
hope you feel better soon.
Jan 
This is what happened to me when the meds stopped working to control my pouchitis.
I hope you are feeling better and it's not that.
Levaquin (levofloxacin) is know to cause muscle and or nerve pain in some people and it causes a magnesium deficiency with cramping. If Levaquin is the only thing that works then take a magnesium pill daily and add VSL#3 probiotic to neutralize the loss of good gut bacteria. This has worked for me for 24 years (no pouchitis!). Ask your doctor if he can substitute Augmentin for the Levaquin when you are having a flare. May work with less problems.