I made a similar post to this one on RMRev, but I wanted some input, so I'm posting it here
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I have hit on a very interesting little quirk in RPG Makers XP and VX. Overwriting any "hidden module" (Input, Graphics, RPG, probably more, but I'm not sure) also alters something in the .dll file you are using, meaning that there's a good chance that your change will affect all the games.
How do I know this? Simple: RPG Maker VX is getting it's Input module from Tons of Addons, in an RMXP project, which I used about three months ago, and then changed my mind on it's Input Script (which really makes no difference, because I can still use the numberpad... And I don't remember why I stopped trying to use the Input script, but it still works anyway. Persistent script, Blizz! It works after you told it not to on other projects! ;D.)
This makes some very interesting things happen if you are stupid enough to attempt them. The biggest hint I had that this dll overwriting was occurring was when, as a test, I "undefined" (meaning I defined it as nothing) Graphics.Update. And the results of that are still in effect, even though I am no longer using that script (In case you wanted to know, the game runs about 1/3 faster than it used to, with no downsides that I know of!)
I'm not 100% certain that it is the dll file that is causing this, but unless someone has another idea as to what is causing this, I'm thinking it's the dll. Also, I'm curious to see if anyone has an explicable reason as to why VX is getting settings from XP, because this isn't making very much sense to me.