It's not something that would be "too hard," it can easily break the menu systems that Vlambeer hastily slapped together with some YAL magic strapped onto it, and multiple UI mods would pretty much break everything. You can use commands if you wish to make your mod configurable, check 9joao6's PVP mod for an example.
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I think your post is cursed. I have the same problem ever since I read your post!!! I have no idea what could cause this :(
EDIT: FOUND THE CURE! Change the game's compatibilty mode. Windows XP Service Pack 2 seems to work, but i'm sure the other ones work too! :)
Try updating your drivers and restarting your computer. If the problem still persists, scream as loud as you can and I'll try to find you.
EDIT: Also try hitting alt+enter to exit fullscreen mode.