After going as far as to reset NTFS permissions and owners and still not gaining any ground I gave it a good think.
Since it was the exact same programs each time, I could install new ones without fanfare I decided to check my security setup which is Hitman Pro Alert and BitDefender Free.
I uninstalled both and everything started working again. I remembered that BitDefender had not just a definition update but also an application update and that's about when my problems started.
I've reinstalled HMP and still working fine, going to install BitDefender shortly and see if it was an isolated issue.
Hopefully this is helpful to someone else down the line.