Old versions of my installer set compatibility mode. I can't remember why, but I thought I removed it. I'll double check that when I get home around to it.
As for the launcher, I'm almost positive it's not doing it. It was written in AutoIt 3, which works fine with xpadder, at least in other applications I've used. All it does is launch ff7music minimized, launch ff7, and then hide in the background until ff7 is closed so it can close ff7music at the same time, to make the whole thing a bit more transparent and seamless. Nothing more than a cheap workaround to make things prettier, but also simple enough that I can't imagine why it would cause that.
Most likely, I meant to unset compatibility mode but forgot. I really need to keep better notes on my stuff, I have no clue why I made some of the decisions I made. At any rate, I will look into fixing it in future installers.