Here's a link to a very reputable drug database, MedlinePlus. It does mention stomach problems as a rare side-effect for Diflucon.
[url="http://www.nlm.nih.gov/medlineplus/druginfo/antifungalsazolesystemic202697.html"]http://www.nlm.nih.gov/medlineplus/druginfo/antifungalsazolesystemic202697.html[/url]
You didn't say if you were later put on antibiotics which usually do cause stomach related side-effects because they kill the "good" digestive bacteria. This can be relieved by eating "live" cultured yogourt while on antibiotics and for a few days after. These yogourts are available at most grocery stores; just make sure the ingredient label says "live" cultures [e.g. lactobacillus].
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