@Snoozy
When you say "minified" what do you mean? Do you mean the game launchers had very small icons, possibly only a small square of a single colour? That sounds like they're OS3.5/3.9 GlowIcons being displayed on an OS3.0/3.1 Workbench... To replace those icons, you need to use something like Rawbinfo to copy just the graphics, otherwise settings get lost, which could be causing your problem. To fix this, try reinstalling the games themselves rather than reinstalling WHDLoad itself.
Also, install SnoopDOS and try run it before you launch a problematic app. It gives a log of all the OS calls made and can be useful to find things like missing libraries or incorrect paths...
Edit: Cool, glad it's sorted for you
