just a couple I can think of. An ear infection perhaps? Or a foreign body such as a grass seed down the canal.
Is the flap itself swollen ( a sign of a burst blood vessel in the flap. Usually due to shaking the head because of other problem such as the infection or foreign body)
Has it been bitten or scratched by another cat? Check for little scabs or crusting areas ( you have probably already checked but thought I'd put this to be more thorouh with possible causes
)
That's all I can come up with. HTH