> - file editor works in "read mode. The whitelist/blacklist files show up
for each individual mail-user but any edits are not saved.

If it were a permissions problem you should be getting errors rather than
simply nothing happening.  Have you tried the file editor on a mode 666 test
file in /tmp?

> - pending files, the pending queue files don't show up.

Can you also confirm that tmda-pending works as "squirreluser", where
squirreluser is whatever user your web server is running as?  Something
like:

$ su apache
$ env USER=virtualuser HOME=virtualusersvirtualhome /path/to/tmda-pending

This will simulate exactly what TMDA Tools is trying to do...

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