There are some notes in the package about extra steps required for authentication if your servers PHP is running as CGI (or f-CGI) and a proggie to generate the proper .htaccess authentication.

Can't say if this applies to you, but you may consider it.

Also, I did have a prob with a SEO module that added a lot of stuff to the .htaccess file. I had to add a rule to ignore rewriting the googlecheckout dir.

Just some ideas.