Wew, the problem is finally solved.
You see, the thing is the mods were getting recognized but the input wasn't, something was blocking off the keyboard input.
I further noticed it in DYOM where I couldn't type my mission name into but rest of the cmds were getting recognized.
Today, I thought to randomly play Spiderman The Movie Game, and by pure luck my Anti-Virus wasn't in Silent Mode since I had shutdown/restarted the computer in months.
There it randomly recognized the program as a keylogger and ALL of my keyboard input was blocked off except mouse. Obviously when I turned it off, all the inputs were possible again.
Now I thought about the SA problem and tried the Cleo Mod with Keylogger Protection off and guess what, it works!
So if you ever encounter some input problem try turning off the Anti-Keylogger of your Anti-Virus Protection Software. Also I did try disabling the software, but the keylogger had to be turned off individually for this to work.
