Thanks for the advice Shane,
So Far I have tried Commodo Cleaning Essentials CCE, TDSS Killer and Rkill, Threats were found and I assume they were deleted. They advise to disable any antivirus programs, which I did although my antivirus automatically kicks back in on start up. Obviously this problem is in two stages. Finding and eliminating the threats and then repairing the damage done. I'll run the programs you suggested to make sure all is clean but then I need to be able to fix (if possible) the damaged files. All the various virus detection programs are building up on my PC. Can they effect each other. Should I remove them after trying them?