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Hey Richard,
Something must have gone wrong during your installation, as SELinux is disabled during the installation process if it completes successfully.
I'll have to do some testing to see if I can see this happen, as you're not the first to bring it up.
Modifying policy is getting closer to possible with Fedora Core 4 and 5 (and Jamie has added a bit of that already)...but even with modifications, there are very likely to be issues with CGI scripts. I've managed to finagle a FC4 system into running everything with SELinux enabled with a half dozen or so changes, and I'm working on getting those changes abstracted into something generically useful (and still giving some benefits of the enhanced security of SELinux) but it's still a little way off. At this point, I still recommend running in permissive or disabled mode.
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I have been watching the audit logs for what violations are occurring and once i figure out what it means i hope i can write some policies to help(as long as they aren't a security risk.