Hello,
Did you have a chance to dig deeper into this issue yet? I'm running into the same problem with a custom box collider in a tk2dSprite with Animator. It will activate the trigger with the player's character controller a few times, then once the player stops moving, it will no longer register trigger events.
Thanks a bunch!
EDIT: This might have something to do with the destruction/recreation of the box collider happening on the collider it previously "triggered" with. I only suspect this, b/c sometimes I am able to cause the OnTriggerStay event to keep firing, however the OnTriggerEnter, never re-fires after a few times. To recreate, create a sprite animtor with an overhand sword swing, with the sword being the box collider, then move a character controller well within the range of one frame that contains a box collider. It should register a few OnTriggerEnter's, then stop, sometimes continuing to register OnTriggerStay's.