I found the solution!
For some reason when I re-imported the Windows games, the "Use an emulator to play this game (primarily for console games)" option was ticked on the Emulation tab of the Edit Metadata/Media... window. I have no idea why this was ticked by default for Windows games.
However, it can't be unticked in the bulk metadata change option, so I had to edit the \LaunchBox\Data\Platforms\Windows.xml file and do a find and replace on "<Emulator>00000000-0000-0000-0000-000000000000</Emulator>" replacing it with "<Emulator />".
Now my Windows games all launch again!
