
I was trying to play DEF JAM - Fight for New York and was getting large blacks columns, so of course I tried different plugins I found out there is another plugin and I think this setting that the other GS plugin I suggested didn't have may be able to solve your problem.
Try This Plugin
GS: GSdx 4600 (MSVC 15.00, SSE2) 0.1.16
-Settings-
Renderer: Direct3D10 (Hardware)
OR: Direct3D9
Interlacing (F5): None [Note: Its for shaking & etc]
-D3D Internal resolution (can cause glitches)-
Original PS2 resolution : Checked
-Hardware Mode Settings-
Allow 8-bit textures: Checked
Do do not be afraid to change the resolution settings because it maybe that the "Allow 8-bit textures" options is what allowed me to see the menu. Uncheck Native > or Use Scaling: Choose "Custom" > Enter in Pixel by Pixel to change Resolution [640x640, 800x600, 1024x768, 640x480, etc]