I have tried to download programs into AT90CAN128 with FLIP. Everything seems to be OK but the program doesn't work. Here are my steps.
1. Program the bootloader with JTAG ICE MKII and AVR Studio in normal way.
2. Enable the BOOTRST fuse with MKII and AVR Studio.
3. Program with FLIP and a CAN dongle, FLIP reports: Verify PASS!
4. Press 'CAN' button and change 'NNB' to 01, BTC1 to 3 to the actual values: 06, 04 and 13 for 250k, CRIS stays to be 00.
5. Change Boot Status Byte and Extra Byte to 00.
6. Press 'Reset'.
In all these steps I got no warnings. Did I miss something?