Well, this is a little bit embarrassing....
...Turns out there was a .net library compiled with CLR 2 which was being run deep within some InstallScript inside the installer. (In my defence, the installer is fairly large!!)
So apologies for anyone thinking this really was a mystery, the dialogue was kinda right! Also, apologies to the guy who guessed right first time and has since deleted his post. It was quite informative on the subject. Feel free to add it back again and I'll mark is as the answer! :)
Andy.