Ok, so I may have jumped the gun here, it seems the board only enters the bootloader when there is no code on the chip. After the first program the board will never enter the bootloader, not over usb or pressing the reset button. Will have to see if enabling the HWBE bit will help this.
DrAzzy:
Am I the only one who reads this and thinks the solution is to solve your power supply problem?
I guess I should clarify, I'm not 100% sure if the issue is vehicle interference or temporary loss of power, but I think it's the latter. I'm using a spring tension terminal block, and I've got a feeling they are shaking around and occasionally breaking connection. So besides putting in the biggest cap I can to supply power in between those breaks, i'm not sure what i could do to fix that.