Solidoodle 2 problem

Hi all,
I purchased a solidoodle 2 a few months back and have had a few problems. The first major hurdle was when changing from a windows 8 computer to windows 7, in Repetier Host the plate temperature disappeared and the extruder temperature was reading zero.
EEPROM in configuration settings was grayed out. I followed the instructions for reflashing the Atmega 644P here:
wiki.solidoodle.com/firmware-flash-update-guide

It worked, the EEPROM was no longer grayed out and it was business as usual.
However, this morning (after a completed overnight print) - the old problem seemed to return and this time, the reflash procedure won't work. Problem appears to be the same, plate temp gone, extruder temp reading zero - EEPROM tab grayed out.

After running Arduino and opening marlin.pde. "Binary sketch size" won't show, and if I upload firmware anyway it still comes up with an error message at the end of the upload. (not found, can't sinc, etc)

I also swapped out the Atmega644 chip with a spare 1284 I have for another project (sanguinololu board, already has everything installed including marlin), and the same problem persists (no change) so I'm assuming the problem is actually something else on the board but I have no idea what.

If all else fails I'll just have to swap out the entire board but obviously that's a last resort.

Any suggestions what the the problem is or might be? ?Any suggestions would much appreciated, thank you !