I myself had a similar problem and I stumbled across a fix that might work. Check the refresh rate and color depth. Mine was on 60Hz refresh and 16 bit color, and I changed it to 75Hz refresh and 32 bit color (dunno why it was set to the former). Ran Jpcsp again and it worked flawlessly. Hope this helps you all 
Edit: narrowed it down to color. Color depth needs to be 32 bit.

Edit: narrowed it down to color. Color depth needs to be 32 bit.