HTAccess - Multi-site/Clean URLs Not Working, Please Help

Hello,

Last week I had a site meltdown, but I've fixed everything and am really digging into
the Drupal stuff so that I can get the full capabilities out of it. My problem is somehow -
I think it happened when I cleared the cache table in my DB, the multi-site function is
no longer working and neither is the clean URL Setting, it's greyed out. And when I run
the "clean url test," I get a page not found error message, and I'm fairly sure it's there.

Can someone please tell me what's going on?

thanks