Just a FYI to others incase they run into this issue.

When installing Quake 3 under MOS I used a Linux Q3 CD. MOS would not recognise the Linux CD. The Linux version mounted as "QUAKEIII" while MOS Installer was looking for "QUAKE3" CD. I went on the shelf and put in my Windows version of Q3 and it mounted as "QUAKE3" and the install continued.

So far I haven't tweeked the settings to much. Only issue I am having as somone else is having is messed up/scratchy sound.