Hi Jenn,
I hope you called your doctor, if you couldn't get in touch with him/her, then I would call your pharmacist. I googled fluconazole and it said that stomach pain, nauseau, etc. are side effects with this medication. Don't know if that is the cause since I'm not a doctor.
http://drugs.emedtv.com/fluconazole/fluconazole-side-effects-p2.html
http://www.drugs.com/sfx/fluconazole-side-effects.html
Let us know what you find out and I really hope you feel better,
Denise