Mega2560 slowly stops responding to input.

Has anyone heard of a board slowly stop responding to input. i.e. - interrupts, serial.read, and digitalRead. When start up the board, everything works fine. But after a minute or two it starts lagging behind. The external interrupts takes a second to kick in. At one point I waved an RFID tag in front of the reader and it would output to the serial monitor line by line but with a long delay between lines. And it would print the lines after i took the tag away from the reader. It's like it caught all the data when it was supposed to, put it into eeprom and said I'll deal with you in a minute. The delay gets to the point where I give up and reset the board. I burned a fresh bootloader with avrdude and uploaded Blink and it works perfectly. I did have a verification error in avrdude. content mismatch at byte 0x3e000 0x0D != 0xFF. Should I set the lock bit to 0x0F when I'm done burning the bootloader?
current fuse settings, i believe they are the ones shipped with the board.
L bit - 0xFF
H bit - 0xD8
E bit - 0xFD
Lock bit - 0xFF
"!!!" bootloader menu (Arduino Explorer) is working.