[support] url rewrite issues with primary links

[sebastian]

Dearest Drupalites,

Having a strange issue with domain rewrites/clean URLs

Moved a website from:

http://basedomain.com

to

http://basedomain.com/test/

[so I can do testing]

Changed the .htaccess where it says:

RewriteBase /

to:

RewriteBase /test

Added the baseurl to the settings.php

For the admin theme I am using Garland, for the live pages I am using a 
different custom theme.

When I view content, they all have links without the ?q= and it works 
just fine.

When I am in the admin-garland theme, the primary links at the top all 
have correct links with clean urls and work fine, like this:

http://basedomain.com/test/home

When I am in the live-custom theme, the primary links at the top all 
have an extra ?q= added to them like this:

http://basedomain.com/test/?q=/test/home

This obviously doesn't work and gives an error page.

Instead of what it should have:

http://basedomain.com/test/home

Does anyone have any idea why my custom theme is having problems knowing 
what the primary nav links should be? How can I stop it from still 
adding the ?q= ?

Do I need to change more in the .htaccess than just the:

RewriteBase /test

?

Thanks you so much for your help!

Sebastian.