FPSE Permission/Role Errors

We have been experiencing some difficulties with our IIS 6.0 and FPSE 2002
server. On one of our websites with several nested subwebs, the default roles
have disappeared. We have since re-created similar roles, but I think there
are some lingering problems. Users of newly created sites are receiving an
error that they do not have permission to publish from FrontPage even though
they clearly have the permission (advanced author) when looking at their
subweb security within the FPSE administration website. I have been
considering doing a remove/reinstall of FPSE on the site but I am worried
about losing all the unique permissions.

Has anyone seen a similar problem? If so, what was the fix? If not can
anyone tell me the ramifications of removing/reinstalling FPSE 2002 when I
have unique permissions on the server and subwebs?

Thanks!