I've done a bit more work to try specifying this problem. Today I've:

  *  Identified another repository where this happens, namely To be clear, the only repository that works is Fossil's. All of mine fail.
  *  Upgraded both my client and server to trunk.
  *  Rebuilt all repositories on the server.
  *  Dumped the offending configs. They are all default and appear OK.
  *  Cloned the repositories from another server with the same results.

Any other advice on debugging this would be greatly appreciated, but as of now I've done all that I can think of on my end.