That's a really good question.
From my understanding, solar flares themselves can't be detected optically yet. Note: It may very well be possible that Kepler can do this, but I don't know. I'm just an amateur.
In one instance of extrasolar flare detection, http://www.nasa.gov/mission_pages/swift/bursts/monster_flare..., it was found by SWIFT detecting high x-rays coming from II Pegasi.
Basically, this is why detecting multiple transits is necessary. Its entirely possible to see some stellar activity that looks like a transit. However, its very unlikely that multiple observations of transits that match each other can be attributed to solar flares.