if i do understand you correct you are using mouse to simulate joystick?
since i doubt double click = full screen <> window mode function will be dropped
there is program called autohotkey it allows to give different or add new functions to mouse and keyboard but its also able to remove some and even make it only work when a certain window is active
so in other words you could make that FOR EXAMPLE:
when you click left mouse button for pc it would be same as you press C but without pc even knowing you press mouse button and that all would be only performed if lets say ppsspp window is active which means you could only do it inside ppsspp window
from that point you would just need bind same function to C button in ppsspp that was binded to your left mouse button with ur mouse simulator
when you dont need it to be C it can be X or U or H whatever ur choice
and that would bypass ur problem
here is autohotkey
http://ahkscript.org
and here are some examples to get you started
https://autohotkey.com/docs/commands/MouseClick.htm
but you also could just google "autohotkey click to button" or "autohotkey mouse to keyboard"
ow and here is if window is active commad
https://autohotkey.com/docs/commands/WinActive.htm
and there are just tons of tutorials on youtube if you care to say you dont understand something
Try AntiMicro graphical program used to map keyboard keys and mouse controls to a gamepad/controller.
http://forums.ppsspp.org/showthread.php?tid=12513
or http://www.x360ce.com