Igor,
Ah, thanks for the CREATE_PATCHES tip. I was trying to cheat and not rebuild the whole thing if I didn't need to, and I wasn't sure about patching the code. So I'll look into that!
Basically the problem is that the default u-boot is configured to respond to both UARTs, and I have a GPS unit spewing NMEA output attached to the UART on the GPIO pins. u-boot receives the output and aborts autoboot, and so the unit never boots. Easy config change, but when the new binary doesn't work..
Thanks again!