I was developing on my local machine (Mac OS X) and moved to a VPS with CentOS 6.5. Problem I'm having is with clean urls. It was working fine on the local machine. However on the vps server, I'm seeing something strange. When I go to enable it, I can go to the config page with clean url (example.com/admin/config/search/clean-urls) and the checkbox is enabled. When I check it and save it, the page refreshes with "The configuration option have been saved." but the checkbox is not checked. I can repeat this process. If I look into variables table, I see the following.
+-----------+-------+ | name | value | +-----------+-------+ | clean_url | i:1; | +-----------+-------+
I cleared cache manually (via MySQL) and through Drupal interface. I checked reports and it is all clean. I looked at logs, but they don't seem to show anything related to this issue. The effect of this is that all URLs generated are ?q=..
Any ideas on what I should look for next?