.htaccess works BUT Drupal doesn't

I've installed Drupal (well, really I installed CivicSpace) into the root of my webspace because it will become the main website once I've converted all the old static HTML pages.

I need the HTML pages to continue to be active for a while until I'm ready to flip the switch. I've set my .htaccess to DirectoryIndex index.htm index.php which allows the old pages to be served up first. I can access my CivicSpace installation by typing in the URL www.mydomain.com/index.php.

Up to that point, all is well. However, when I click on any link within my CivicSpace theme, it takes me to www.mydomain.com/?blahblahblah instead of www.mydomain.com/index.php?blahblahblah

I can't use my CivicSpace installation because of this. How can I correct this so that I can have both the old HTML site and the new CivicSpace installation working simultatenously?

Thanks for any help! I'm really lost here.