Do you have your kernel sources uptodate wrt sources?
Long ago there was a problem with the scheduler that allowed fossil
to eat the cpu (because of a sleep(0) IIRC).

I also run a fossil updated from sources and it runs just fine.
Have you double checked diff'ing w/ sources? (I'd check fossil and kernel).

Can you try using a fossil that runs off a different disk? (Or perhaps
using a kfs on the disk and starting a fossil running from a file), just
to see if it's a sd thing (I'm using ide).