We are re-doing the look and feel of our site and have created a new theme for it. The problem is as long as the Permalinks Settings are set to default the pages load fast with no issue. As soon as I set the Permalinks Setting to custom structure and specify the following /%category%/%postname%/ the site load time increases. The pages take a really, really long time to load.
The interesting thing is if I switch make to the old theme, the pages load fine even when custom structure permalinks are specified.
Any pointers on how to troubleshoot what could be causing this would be much appreciated.