FTL:AE Steam version not working but FTLGame Folder works.

[Physics]

So I have found something weird for me, after installing some mods which broke my game I spent a long time relentlessly de-installing and re-installing the game, verifying the games files, deleting the save, editing stuff and now I have fixed it in a weird way.

When I launch the game on Steam it will load and when the load bar fills up the game will just crash and quit. So I opened up the Properties tab of the steam version and browsed the game files, and I saw the "FTLGame" file inside the game files, so I decided to click it and open it up. Guess what?
It opened up the game and actually loaded it, no autoquit on splash screen, no nothing, just AE version without Steam.
Now the real problemo is the fact that I want the game to run on Steam (I need the overlay) but I'm greatful that it works anyway.
So anyone know what the hell caused this?

-Cheers





EDIT:EDIT:EDIT:EDIT

I Fixed it! I opened up the FTL Game file and that worked, closed it, pinned it to my Toolbar, that broke so I decided to open it on Steam and now it works..
Wha-how-Why?
Anyway, I would still appreciate your thoughts on how this happened xD