Right basically I have upgraded my php installation to 5.5.4 and in doing so I have broken something >.<, The front page will load however trying to go anywhere else will just display the default 404 page from apache.
I am running ubuntu 12.04 if that helps.
Any ideas guys, this is frustrating the hell out of me >.<
Couldn't figure it out so I have just gone through a painful process of reverting my php version back to its original state which seems to have fixed it, it must have had something to do with the build I was using but its too much hastle for what its worth