Admin page - Access Denied

Please advise on the following process. I've read up on a lot and at this point, I'm a bit lost still. I was planning on reinstalling the drupal installation to see if it would work... Also, I use Clean URL's.

I was attempting to move a subdomain (beta) drupal installation UP into the root (www). I say up because on the hosting company's server, subdomains are created within the (www) folder.

Before I did this, I created a new subdomain (charlie) to test. Copied all files from (beta) to (charlie). In addition, I changed the $base_url under settings.php (as an article as advised). I'm keeping the same database. All seemed to work. I tested by adding new content to verify, logging in and out. No problems.

So I decided to copy (charlie) into (www). I updated the $base_url. But things weren't working now. I later realized .htaccess file wasn't moved. Since (www) already had something written in the .htaccess file, I simply appended the .htaccess from (charlie) onto (www). Then the Clean URL's seemed to start working (I verified simply by clicking on URL to nodes and noted in the status bar that it was referring a "clean URL".

However, when I logged in, I got access denied (www.example.com/admin). However, (www.example.com/admin/settings) worked! Baffled. So I disabled Clean URL's and the admin page now works (www.example.com/q?=admin) along with everything else. But other errors come up that I think are contingent on Clean URL's to work (just how I coded, I guess).

Does this ring a bell for anyone? Any advise would be great appreciated. I'm not sure where else to read.