Mark,
Thanks for the reply man. I'll give these suggestions a shot when my new board comes in.
Ive tried ruling out it being a heat issue, as yea, i thought thats what it was right off the bat. For one, pololu says you can push 1A without a heatsink. I run this thing between .9-1.2A, as torque isn't really required for what i'm doing (sweeping a laser beam).
In efforts to rule out heat, I grabbed a RAM chip heatsink and glued it to the pololu. It does heat up, but not too bad to the touch. Also, I placed a fan right next to it and gone as far as timing the moment of shutdown to see if it varies based on heat.
Now you would think IF its heat, that after the initial shutdown, if i waited long enough it would work again, but, not such the case. Doesnt matter if i wait 30 seconds or 30 minutes, i'm stuck with a moot project, unless i simply reupload the code.
The other 2 reasons i think i've ruled it out is, ive seen this thing on a meter go into shutdown, and the current would climb REALLY high, then stop at 0. When it stops now it holds precisely at 1.2A, just stops moving. Also, if i hook this thing up without an arduino, just manually wire all the logic to 5V and GND as needed, it will run indefinitely.
There are 2 9V outs on this beefy psu, im thinking this time around i'll run the arduino by itself off of one rail, still with the decoupling caps as you suggested, and see if i can come up with another 5V supply for the chip other than the arduino, so that the arduino is simply providing nothing more than logic, as right now i was running the arduino powering 5V to the pololu.
Thanks again mark!