I've reproduced it (or something similar)
I've been able to reproduce a problem, although it seems to be the opposite of what you are seeing. I suspect it's the same sort of thing, though.
If I exit Opus completely and then double-click the excluded folder on the desktop, it will cause Opus to re-launch and then open an Opus window for the folder.
If Opus is already running, however, then double-clicking the excluded folder causes it to open in Explorer, as it should.
I've reported this to GPSoftware so they can look into it.
Workaround
If you want to you can solve this problem by having Opus always running in the background. You can do this via Preferences - Launching Opus - Startup by copying the settings from the screenshot below. They will cause Opus to run in the background but not open any windows at startup.
Alternatively: Setting the folders to use Icon mode
If you instead want to use Opus to display your Games and Tools folders in Icon mode then you can do that using Folder Formats.
Go into the Games folder, switch Opus to Icon mode, then use Tools -> Folder Options and then Save -> For This Folder. That will tell Opus to use Icon mode whenever you enter that folder. You can then do the same for the Tools folder.
Screenshot
Here's the Preferences screenshot mentioned earlier:
