What's going on?

[664a683d87dd2Primitive Primeape]

So I reinstalled Shock 2 because I was bored. I patched it with the Tool, made it FM ready, downloaded some replacements and Shock 2 Infinite.
I rescaled the HUD and rebinded some keys to my personal liking. I start the game and my keybinding isn't applied. Oh well, I quit the game. I went into the user.bnd with notepad only to see that my custom binds were completely gone. So I put them back. Restarted the game, bindings still not applied. I ignored it and decided to play anyway.
And of course, none of the mods worked. Only xdiesp's Infinite mod because I placed that in the FM folder.

I installed Shock 2 in the root of C:\
I am admin of my own PC
This is not the first time I reisntalled the game this month, but it is the first time THIS happens.

[664a683d88020voodoo47]

maybe start all over again, and try using a modmanager this time.

[664a683d88115This_is_Xerxes]

You could try binding the keys with vanilla and then installing mods.

[664a683d88215Primitive Primeape]

I forgot to mention that I indeed used a mod manager. I used Blue's as I always do.
And what Xerxes said, I tried that to no avail.

EDIT: Works now.