Without a schematic or wiring diagram its really hard to pinpoint the problem. Based on your description it seems like a power issue. Without knowing what Arduino board you have, I can only speculate, but I bet your onboard voltage regulator blew. Those linear voltage regulators are super inefficient, especially when they have to drop a lot of voltage 12->5. That voltage drop is also dissipated as heat, super bad if your not using a heat sink. Also I think those onboard v-regs have a supply limit of 400mA? (don't quote me). So if your powering anything 'from' the Arduino board that exceeds that rating, your gonna have a bad time.
Depending on the chip set, the Arduino is really only rated for 5vdc or 3.3vdc, the onboard regulator is rated at 12v, not the chip. So don't connect your Arduino IO to any voltage source greater than that without proper level shifting. You might already know this, but I'm just covering all the bases encase you don't.
If it is the regulator, you can do one of three things.
1) Swap out your Arduino board with a new one and see if the problem persists.
2) change out the onboard regulator (it's pain if you don't have the tools) and see if the problem persists.
3) Hook a buck/boost regulator up to the 5v supply pin of the Arduino and see if the problem persists.
Tag me if you need any help/advice.