It's not a huge surprise that flares dazzle IR cameras, no more so than it is that searchlights take away night vision adaption. The direction the flares go is the opposite to that of an incoming missile; however, you still can't see little distant sparks through the big nearby ones. Not firing repeated flares because it can still see flares should be a relatively easy fix.
How does it react to being dazzled with IR lasers? Does it fire off all its flares like a christmas tree, potentially providing a detection method? Then again... from behind it's bright and hot anyway, providing a detection method.