Yeah tried all that first still not working, it seems to install it then just replace it with the stuff I deleted.
Trying to install manually from the cab files.
EDIT: Still not working.....WTH?! Keeps replacing the newly installed files with the old ones...
EDIT 2: Fixed this by installing Fl to another directory (C:\...\Freelancer2\) Not sure why I have had to do this, but that is how I solved it in case anyone else gets this problem.