Unfortunately, after further testing, I figured out that I was being a bit silly...

It was OpenIV.asi 'causing' the issue because when I'd installed the IVPack Addon Cars, that must install a different car variations file or something. I'll have to do some digging and find out which file it was.

No idea if it's related, or if an update to the game has messed things up, but whenever I spawn (for example) the Tyrus (Supers class), if I use Menyoo or any other menu, I can't upgrade the vehicle apart from the most basic of things. I know prior to the Import/ Export update it seemed to be fine, but maybe I've installed other mods that are indeed as you've suggested, causing some sort of conflict.