My issue seems to be that SwitchRes isn't using the correct resolution; or possibly the correct resolutions don't exist. I'm not sure. I'm probably doing something daft 
Switchres is working fine as far as I see. The resolutions are the expected ones provided you're in a 31 kHz setup. The wrong refresh rates are from vertical games which use 512 lines (256 x 2, or 512). You simply can't get 512p@60 Hz at 31.5 kHz.
So either increase the horizontal frequency:
monitor custom
crt_range0 31400.00-
31500.00,49.50-65.00,0.940,3.770,1.890,0.349,0.064,1.017,0,0,400,512,0,0
(The remarked value is the default for arcade_31. Raise that value at your own risk)
Or, tell Switchres not use 512p:
monitor custom
crt_range0 31400.00-31500.00,49.50-65.00,0.940,3.770,1.890,0.349,0.064,1.017,0,0,400,
480,0,0
(if you put that in the vertical.ini file it will work and still don't affect Irem games, MK, etc.)