I had the same problem and applied a quick fix against skyeye-1.2.0-RC4.
Its ugly but nevertheless should serve the purpose. I used a fresh
u-boot (version u-boot-1.1.3) configured with at91rm9200dk_config.

Thanks a bunch for the patch. You made my weekend ;).

I can now run u-boot for at91rm on skyeye(compiled for DBGU instead USART).

Cheers
rohit