The emu can only switch to 640x480 if you have a corresponding "Modes" line in your XF86Config[-4] file.
Code:
Section "Screen"
Identifier "screen1"
Device "device1"
Monitor "monitor1"
DefaultColorDepth 24
...
Subsection "Display"
Depth 24
Virtual 1280 1024
Modes "1280x1024" "1024x768" "800x600" "640x480"
EndSubsection
...
EndSection