Control Issues in epsxe

After downloading the program, i immediately downloaded isos for some of my favorite games (which i do own, but have been packed away for some time now and i have no idea where to even start looking for them). Upon finishing the downloads i unzipped the files using 7-zip file manager. The first game i played worked fine (FFVII) using both default keyboard controls and a foreign gamepad i bought at an electronic store in Japan; however, when i tried to play the next game (FFVIII) the controls did not respond. I waited, tried resetting the controls again, tried working with the default controls, tried unplugging my gamepad, tried literally everything i could think of, some things that i didn't even think would have any effect, the controls did not work. I doubt this effects anything, but I have tried this using both the PEC program video plugin and the Pete's DX6 D3D Driver 1.77 and reconfigured both plugins several times. I finally dismissed the problems and moved on to another game (Chrono Cross) and the same problem re-occurred. I continued to try other games and other discs of the same games and the problem is constant through all the games i tried, except for FFVII. Any suggestions would be much appreciated. As far as what I have seen of the emulator, I love it. FFVII never ran so smooth on my psx and it looks 100% better on my PC than on my TV.