I had been using a very old board definition, and when I updated to the latest, it changed all the pin numbers around. I guess this was enough to turn SOURCE and SINK on at the same time for the GPIO I was using. GPIO1 had already fried months ago when I was first trying it out, but all the others worked. Now, none of them work.
I ordered a complete unit to replace it, even though the processor board and the CAN interfaces still work. I can see why they changed the GPIO design for the release board.