That's a die off symptom. Don't be fooled by it. Your symptoms will continue after Flagyl for a while, becuase what you experience as "symptoms" as toxins released by dying amoebas. Those are the very same toxins that they release much slower when they are digesting their way through your body. Headaches, nausea, diarrhea, exhaustion, and all kinds of pains (in areas where amoebas took hold), are normal. If you took it again, you'd notice that symptoms are less pronounced. The third time you'd have no symptoms at all, as most amoebas would've been killed by then.