First, thanks to everybody offering tips and help. The good news is that the problem is solved.
I couldn't wait, so I finally decided to learn a little FreeBSD kernel debugging. After reading lots of not very comprehensive man pages and other guides, I got a 4.4 kernel compiled with ddb and set up remote debugging over the 2nd serial port with gdb. Again, after reading even more on using gdb, I set a bunch of breakpoints a did a little tracing and got the problem localized to a PCI configuration problem, probably a undocumented hardware bug in the Geode SC1100 processor combined with not very smart PCI config code in FreeBSD. I have patched FreeBSD to boot on the net4801 board, more details after I know exactly what's the issue is.
Lesson learned:
Advanced FreeBSD documentation sucks if you're not a kernel hacker, but remote kernel debugging works great and are actually kinda fun....
Regards,
Soren Kristensen
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