Having issues with the emulator after playing a while

[The Phoenix]

Okay it sounds like you activated a Postprocessing shader,
Go to settings in PPSSPP, under the Graphics Tab, Click on Postprocessing shader, and see if its currently ticked under CRT Scanlines, or anything else, if so click on Off to turn that feature off, that should solve your problem, but just to make sure, click on Back, then Exit the emulator.
This will then save how the options are currently, so next time you run PPSSPP, it will re-use the same options as now.