It's because the tool patches plugins.js poorly. Depending on the formatting it'll just throw commas all over the place which makes the game fail to load plugins altogether. Some games just fail to launch if this happens, some launch but with massive bugs.Also some games don't even run at all if the cheat menu is applied.
You can fix this by restoring [GameDirectory]/www/js/plugins.js to the version you downloaded, then manually appending
{"name":"CheatMenu","status":true,"description":"External cheat window, for easy item and variable modification.","parameters":{}} to it.