I thought I'd update with my findings in case it may help others in the future. I, eventually after a few hours of researching found that the problem was, in fact, to do with malware before originally scanning had infected my computer with registry entries which were preventing pretty much any antivirus software to run by hijacking the .exe executable. This was done by creating an undeletable registry entry in the Image File Execution thread of the registry.
To rid me of this was impossible during boot due to it tying itself with the OS. So I had to delete the startup Hijacks using a great freeware application called AutoRuns which gives you a huge comprehensive list of everything that starts up and it's associated registry thread. Simply delete the autorun entries then reboot. After that, I was free to delete all entries and everything loaded perfectly then
Just thought I'd put up my experience as it may affect others, and I imagine this could happen with any file type too.