I would definitely go back and describe all this to your vet.

Metronidazole (Flagyl) can have some side effects, which is what I think you're seeing there. Presumably your vet thought he was suffering from a Giardia infection... I remember reading recently that treatment with Panacur (Fenbendazole) - a gentle & effective wormer which can be bought over the counter in some pharmacies - had been found to be much better at treating giardia and has fewer or no side effects.

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