I am not sure what is going on, but I am having the same problem with a Mega2560 Rev3, a Mega2560 Rev2, and a Due. Is there a problem with the sample code for attachInterrupt( vector, ISR, mode)? In reading the instructions the vector has to be changed to the monitored pin number for the Due, but other than that, the code should work the same. Can anyone provide some insight?
It would be better to start a new thread, even though the problem looks similar. The OP had a Due, you have a Mega.
Post your code please.