There have been too many complaints on the forums about people having trouble installing WPMU. A number of these are on Cpanel administered sites.
Until this morning I had never used Cpanel, but thanks to James Farmer I had my chance.
Here’s how I debugged the problem with installing WPMU on Cpanel sites.
This problem probably extends to any web based installer that creates a .htaccess file in the root directory because Cpanel creates an empty file of the same name.
This is a problem because the file is owned by the user running Cpanel, not the web server. You have to change the permissions of the file through Cpanel, or ftp in and delete it.
Give me a shell any day.