Help in programming the Atmega1284 with maniacbug-mighty-1284p.

That's what I am saying. Poor layout, poor wiring, poor who knows what.
I have made over 50 1284 boards in various designs - DIPs, wirewrap, surface mount - and I have not had a problem 1 time.
Not even with older date code parts, such as the 1050 I demonstrated with tonight.
Bootloading with Atmel MKii, and serial downloading with a couple of different FTDI based modules.