After recompiling apache and php for new module support I found that the script aliases on httpd.conf like:
ScriptAlias /webmail /usr/local/cpanel/base/wredirect.cgi
and such don't work. suexec log says:
[2004-07-07 14:26:45]: error: target uid/gid (32003/504) mismatch with directory (0/0) or program (0/10) or trusted user (0/10)
Not sure why all of a sudden it's not allowed access to /usr/local/cpanel/base. It appears that during the upgrade suexec didn't get seeded with correct doc_root and other information to run properly.
Doing easyapache I thought I saw mention of 'patching suexec'. Does cpanel hack it to allow it to function in such a way that it's originally not supposed to?