Access Denied with Clean URLs Enabled

Hi

I have Drupal 7.7 running on bluehost.com. For the primary domain they do not provide the possibility to have it in sub-directory of public_html. Nonetheless I managed to do so with .htaccess files. Everything works fine but when I turn on clean urls, in some cases I am getting access denied message (for example when I try to check for module updates). With Clean-urls switched off it works perfectly. Could some one point me in good direction, what to do to solve the problem.

Thanks

Darius