I think the reason this happened was because I added a debug check, in-game, that tries to determine if the game is running with elevated privileges (i.e. in Admin mode).
This check runs net session with no arguments - a read-only command that only succeeds if the program is an admin, and fails otherwise. This command would normally be used to see if the computer is being used as a remote device.
On both success and fail, the check does nothing afterward. It was originally going to be used to skip a puzzle by cheekily running the game as admin, but I may end up removing it entirely.
Also, the check always fails when the game is running in the browser, so even if you don't trust the downloaded version of the game, you can still play it in your browser.