Our guild website already has a rather complex set of re-write rules.
To start with, both roster.<hostname> or <hostname>/roster get re-written as we break up the directories into different accounts for different admins to control.
Because of this, the default .htaccess file just wasn't playing nicely with the other re-write rules (namely our.guild.org/roster isn't really in our main web directory)
So for those with a similar problem (if this makes sense to anyone other than myself) might want to consider using: RewriteBase
eg:
RewriteBase /roster/
Add that to the default .htaccess file provided with wowroster and, if your webserver is as overly complex as ours, all is well. Sadly, it doesn't fix uniuploader, I wonder if that's a firewall problem