The best I can say is maybe the OpenGL implementations are different for each manufacture, as far as I know I don't think shaders work correctly on Intel (and ATI) cards and even though they are checked the emulator will automatically disable them behind the scenes when they fail to compile a successful result (you can see this in the logs on the INFO setting usually), Have you tried to disable shaders on the nvidia card to see if it produces a similar result?
Try Out JPCSP Launcher v1.8.0.4 | How to post a log