Flagyl can have very serious side effects and best used sparingly for short amounts of time. I did a quick google and an adverse effect of flagyl is frequent or painful urination, so that definitely could be it. Flagyl temporarily paralyzed my girl long ago, and it made my boy stumbly after 3 days on it. My girl now is currently on it, once a day, every other day, but the internal medicine vet is concerned about its use.
Something else like amoxicillin might help, or try a bland homecooked diet (say beef and overcooked rice, etc.) There are other things that might cause the diarrhea other than giardia.