Long story short, if I 'cd /usr/src/gx86/app-crypt' and run 'repoman commit --if-modified=y', it works fine. However, if I run that in top-level, I get: cvs [update aborted]: no such directory `app-admin/cgmanager' [CRITICAL] !!! cvs exited with an error. Terminating. So it clearly tries to do something to non-checked-out directories but only when run in global repository scope.
Nevermind. Seems to be caused by some stale entries in CVS/Entries.