Well... it works now. I manually replaced the bootloader file, FWIMG01.DAT, and Rockbox fired up afterwards.
The bootloader that gave the above error was placed by rbutilqt.exe, I guess it has a different version of the bootloader.
Speaking of which rbutilqt.exe is buggy as hell, I haven't been able to use it without it crashing at some point and it constantly consumes all of my CPU, but I guess thats a subject of another forum.
Anyway, all good here now. Happy Gigabeat cF 32GB owner over here.
[EDIT]
A followup... The bootloader versions differ and function differently. The one I used to use with the 4GB CF card had a gray background and booted Rockbox after bootloader USB mode.
One I use now, off the wiki page has a black background and turns off the player after bootloader USB mode without attempting to boot Rockbox.
It works, but why all the confusion with undocumented bootloader versions?