Today, as expected, the AVR dragon and ATMega324P STK600 routing card arrived.
However, since I'm in the middle of trying to get my GLES2 test program working properly on the Beagleboard, I am going to finish that task first, then switch over to AVR debugging.
I am pretty close; I've got the purple rectangle displayed on the beagleboard, but it is the wrong size. I've tested my view and projection matrices on linux/x86 and it works fine but I am kinda using an odd projection matrix that maybe requires a lot of floating point precision. I am going to redo my projection matrix to a very simple one and see if that fixes it. If that is the solution then I am done. I'll test tomororow morning.
UPDATE: I was wrong, it is working fine. The reason I was confused is because my linux/x86 setup was running at over 5000 FPS (Geforce 8800GT) and the beagleboard is running at about 120 FPS. Once I enabled sync-to-vblank on the linux/x86 box, I was seeing comparable results (it ran at 60 FPS). It's good that the beagleboard is running at 120 FPS but not so good that it's doing it drawing just two polygons hehehe. Maybe there is more here than meets the eye.