I'm sure I'm doing something wrong, but this is one of the games I have where Shortcuts just don't seem to work (the other being Populus 3) and after running the ipxrouter, it now says it can't run it where before it was claiming it couldn't find the .exe.

I've managed to get it working now by loading it up from the .exe, doing ctrl+alt+del and then pressing cancel to get back to the desktop and re-enter the game where the graphics are fixed. Funnily enough, if I launch the game immediately after installation (in the menu after you've installed the game) I get none of these issues. It loads up right away, no graphical issues and everything is fine.

Anyone have a clue as to why the shortcuts don't seem to work?

The only difference in running the game directly from the installer is, that it runs explicitly with administrator rights.
Try the same when starting the game with the shortcut. Right-click it and choose the option to run it as an administrator.

Worked brilliantly! Well so far I've tried KKND, but not populus yet. Still goes funny when I try to load it in steam though, but getting the game itself running well is the most important thing.

You're welcome.