Hmm, have you actually extended the Windows desktop? So when you go to the regular windows display settings right now, you should see two separate monitors called 1 and 2, not the combined 1/2 single screen. (If you hadn't extended the desktop before, do it now, then take a look at the res on the CRT. If it's 640x480, try plugging in the CRT.)
(EDIT: actually, if you are only just now extending the desktop, turning EDID emulation off and back on again might be something to try, if the res looks wrong on the CRT)
Assuming that's not the problem, let's try this. Under the Monitor Settings tab in VMM, select Generic_15 rather than Arcade_15. Then, in the Video Card tab, disable an re-enable EDID emulation for the Analog_0-VGA port. Then, on that same tab, under Device near the top, select the Generic_15 monitor, not the LCD one (the LCD is currently set, called PLB2403WS). That will set the target for VMM modelines to be the analog output. Then install modelines as provided by the user_modes.ini file, as per the guide.
Restart the PC, and open ArcadeOSD on your LCD. Hit the number "2" key, hit "1", hit "2" again. If that worked, you should now see the ArcadeOSD screen on the LCD again, but the line near the top should have changed so ArcadeOSD is no longer targeting the LCD but the other display output, the crt. What shows up in the video modes? If you can switch to a 15kHz mode, say 640x480, you could plug in the CRT and see what gives. ArcadeOSD will disappear onto the CRT at that stage anyway. Hit Esc to go back at any stage in ArcadeOSD. (there might be two 640x480 modes now, one called 30i and one called 60i, but nevermind that here. Both should work, but if you're on one, try changing to the other).