Follow these steps:
- Run VMMaker. In monitor's tab, select "Arcade 15 kHz"
- In Vmmaker's command line, type:
modelist import
mode add 648x486@60
modelist install
- Exit VMMaker (don't use the Generate Modes nor Install Modes buttons!)
- Now, in Windows display properties dialog, or in Arcade OSD, set the desktop's resolution to 648x486
Why 648x486? Because this way you don't overlap your existing 31 kHz 640x480 (I think it's good you keep this one as 31 kHz considering the monitor you have and some systems will benefit from it, and also having it editable by not making it the desktop's mode).