New plan :|

There's no reason mIRC actually has to be installed in Program Files, since it's a copy+paste job not a proper install...
And there's a pretty damn good reason to install it anywhere else :|
Microsoft's ridiculous security settings mean you can't modify any files in Program Files...
Which, I guess, is the reason mIRC (and other programs) actually run in that stupid Roaming Appdata folder somewhere else...
This is totally crippling for mIRC, especially if you're trying to do any scripting...
Without being able to edit the mirc.ini file, it can't remember any of the config settings... Without being able to edit any of your script files, when you restart mIRC they revert back to whatever they were when originally put into the Program Files folder...
The whole 'actually run in roaming appdata' thing is beyond ridiculous, because it means going and looking at all the files where you installed your program actually tells you nothing at all, because it's not using them :|

Solution:
Run mIRC from somewhere else... I now have all my mIRCs in My Documents, and suddenly everything is perfect...
I kept the -r parameter in the shortcuts just in case but I suspect I don't need it any more because they should just run in their install directories automatically...

My advice to anyone who's still reading at the end of this rant:
INSTALL MIRC ANYWHERE APART FROM PROGRAM FILES :p