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Hey Adam,
Sounds like a SuExec problem. Check to be sure you ended up with a Virtualmin-provided Apache package:
rpm -q apache2
It should have "vm" in the release field of the package name. If not, something is wrong in the installation process that allowed your old SUSE-provided package to stick around. An update with yast might do the trick (not "yast online update" or "you", which uses a completely different format of repository that seemingly has to be created by a SUSE system, just the yast package manager update process...I know it's really confusing, and I've yet to figure out why SUSE has so many different an incompatible mechanisms for updates and package management).
There shouldn't be a cgi-bin in public_html by default--it goes in the base domain directory. There are security implications to putting it into public_html.
That's not to say there aren't permission problems with the current configuration, but cgi-bin is in the right place for the way things should work in the default Virtualmin configuration.
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I have the .vm at the end.
But whenever I put a cgi script in the cgi-bin directory, the browser tells me it can't be found.
if you have a quick hello world cgi script handy, post it so that I can try it and I'll create a new virtual domain and try it out stock.
HOw to you update with yast? i know how to upate the suse system using Yast, but not what your saying about yast package manager.
Adam,
Take a look at SuSE 9.3 update steps in virtualmin questions forum. The same is used for SuSE 10.0.