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Well, Just a little update.
I have come back to this a few times getting frustrated each time...
I have found the problem, but according to datasheets, there is no problem...
The issue, I believe, has something to do with the watchdog shutting down the controller. Ive retested all hardware and everything is working perfectly.
If anybody feels up to it, the old processor was an Atmega644A and the new processor is the Atmega1284P. If anybody can find any differences, I would LOVE to hear about them.
-Adam
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