I encountered a similar problem with the same component. When using the -UA versions, the UART download works fine. However with a -CA, I always have a problem. I am using a VECTOR CANCARDX (PCMCIA) interface. The FLIP software (same version as you are using) always gives me a CAN INIT FAIL. The interface card functions correctly whith the CAN-ANALYSER software from VECTOR.
Even the ATMEL distributor in Belgium doesn't know what they are talking about ....
If you have any idea's ....

Regards,
Eric Moeskops