V-sync in the chassis is vertical hold, nothing to do with flicker.
First of all, GM should be using a progressive mode even with super resolutions, not an interlaced one. At least, it should for games that would natively display that way. Pick something like SF2 or Final Fight, or anything you know is progressive (224p through about 256p) and make sure the info- and nagscreens are on - those being the blue ones that come up at game launch showing the game title, native res, res that switchres has chosen, etc.
What do they say? For Final fight you should see 382x224 as native, and then (probably, if you followed the guide) 2560x240p as the screen res chosen.
If the system is NOT using a progressive mode, next step is to check ArcadeOSD to make sure the 2560x240p mode exists in the system. Test it there to make sure it works. If it's there and working, but GM isn't selecting it, then your GM settings are wrong. For newer versions of GM, IIRC, you just follow the crt_emudriver guide and just dump GM where you want it. By all means go through the GM install guide on Calamity's site (same place as the guide you linked above) but be aware that the stretching options are now different, and that the Resolution line should be set to 2560x0 and the Super Resolutions Trigger (or whatever it's called) should remain at 2560.
If the 2560x240p mode doesn't exist, you didn't follow the crt_emudriver install guide to the end. Start over.
If the mode is there, and GM is using it, and it still flickers, however, there may be something amiss with the monitor. Progressive modes shouldn't flicker. What Jamma interface are you using? J-Pac?
There may be ways to reduce flicker in interlaced modes, and they might help, but I'm a backyarder so anything I suggest is going to be suck-and-see. As for 640x480@30i flickering less - I have no idea. Does the 640x480@60i mode not behave the same?