Seems my webhost has 'blocked' .htaccess files, or at least screwed them up - found my website has been broken for some time, as my use of .htaccess files only matters when you browse off the main page. Regardless, I have switched off search engine friendly links so it now works again, though this is not ideal and certainly not permanent.

Update: Problem now solved. Though they broke it again a few days after I solved it so I had to re-solve it. They also lied about the cause of the problem. Accusing me of running Windows and having a virus that is adding .htaccess files when my problem is the deletion of .htaccess files (Followed by them disabling the ability to recreate them.), plus I'm running Linux anyway, which makes their bullshit kinda obvious.