I also get diarrhoea when on cipro, though it usually passes after the first few days. I found that when I took it on an empty stomach (1/2 hr before food or 2 hrs after food) it happened less (whenever I forget and take it too close to a meal I get sick again). Does yours come with the warning not to have milk/antacids/iron supplements within two hours? Those things reduce the absorbtion so more of it might pass through your system and upset things.
Sorry if this is tmi, but once when I was put on the 750mg dose I got very bad diarrhoea and i could smell the meds really strongly when I went to the bathroom. It was because I was on too high a dose and my body couldn't cope, so if all else fails talk to your Dr and see if the dose is too high.
side note: I also get nausea with cipro, I found that sucking on a mint made it dissappear like magic <img src="i/expressions/face-icon-small-smile.gif" border="0">
AJ