Alright, have you had l.e.d. confirmation when teensy was operating properly during boot up?? If so, and now the light is failing then you said it yourself, it's either it is not pleased with the currant .hex files you have on your payload, and they may be corrupting your board.
Try a different flash. Also If Atmel/Flip is recognizing the teensy board then the board is not shot completely. You know you have a operable board if your flash is successful then the on board is functional. It may be on the verge though, these boards will fail with no fault of your own my friend.
As far as the red light, try soft reset/restore databases. Also, speaking from experience, the louder your fan gets the closer you are to board failure due to fan malfunction, or a a slu of other bs. FYI It's blowing harder to compensate for your motherboards increased heat, But don't get me wrong I had a backwards comp. that you could fry an egg on and its still cookin. On the same note I've watched them blow hard and load and fail. Hope I could be of some help GOOD LUCK!