OK, the good news is that I've managed to stop this error occurring on my system. I still get a load of strange DOS boxes, flickering and so on, but the export works and the games are playable when uploaded.
The bad news is that I'm not entirely sure what fixed it, as I spent an hour changing and uninstalling things, after which the problem seemed to be solved. I can narrow it down and say the fix must have come by doing one or some of the following things:
* Setting Windows Explorer to show hidden files & folders
* Verifying Application Cache for CS2 Within Steam
* Disabling Steam In-Game Community
* Uninstalling Steinberg CuBase and associated drivers
* Uninstalling GameMaker Steam version (in case of sabotage)
* Uninstalling All Non-Valve Games from Steam
* Uninstalling Skype Click-to-Call
* Uninstalling EA Download Manager & all games that need it (Spore etc)
* Disabling Every Plugin, AddOn and Theme within FF & IE (left Chrome alone)
* Using Driver Sweeper to remove any outdated graphics drivers (Nividia)
(edited for spelling)