For those who have the same problem as me, here is the workaround as suggested by KrossX:
Download
NirCmd (32bit or 64bit. I use the 32bit because the executable is smaller: 36kb).
Put the "nircmd.exe" file in the same folder you have the "pscx2.exe" file.
Now create a new text file (*.txt) and use the sintax like explained below:
nircmd.exe setdisplay width height bitdepth: this will run NirCmd and set the resolution and bitdepth to be displayed;
pcsx2.exe: starts PCSX2;
nircmd.exe setdisplay width height bitdepth: it will set the resolution and bitdepth when the program specified above is closed. Useful to return to the resolution you had set in your desktop prior to running PCSX2;
Here is the sintax I use:
Code:
nircmd.exe setdisplay 1600 900 32
pcsx2.exe
nircmd.exe setdisplay 1366 768 32
Save the *.txt file with the values you need, name the file and then change its extension to *.bat.
Put the *.bat file in your PCSX2 folder and run it.
Now PCSX2 can be optimally used without having to change the desktop properties at all. NirCmd sets the resolution really fast and without prompts like "Is your display working?" or "Do you want to keep the changes?". If needed, the *.bat file can be later edited by just right-clicking it -> Edit.
Thanks KrossX again for the help.