I'm starting to realize that that motor shield is an utter POS... I'm going to try splitting the power so the Uno and the Motor shield are using separate battery packs. Hopefully I can figure out how/where to cut the traces on the board to do that....
With only 6V total from the 4AA's, it just seems like teh second the Motor shield needs extra power, it causes the spike which browns out the Uno, which really wants 7V anyhow.