On the big project waiting any amount of time doesn't help, I
still get the errors - it's like fossil remembered the state
with the wrong line endings.

Time has something to do with it - I'm fossilizing an old
project from out of tar.gz files, so there are lots of quick
commits with a large number of files, and the files have
old timestamps.  I'm guessing the previous commit already
messed it up somehow.

The files have windows line endings, but I'm on linux, although an old
one:

<verbatim>
Linux 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:16:33 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux
</verbatim>