I implemented your advice, cools and Calamity, many times and with some variations. Thanks for your help, but unfortunately nothing worked to get Groovymame selecting non-interlaced modes for vertical games. I'd try tearing my hair out if I thought it would help.
I would delete all ini files (except the presets), and generate a new mame.ini with "groovymame64 -cc". Then start a fresh VMM session and load generic CRT TV specs, though specifying aspect 4:3 . My desktop was rotated as well, so I'd select "vertical" and click the box for rotated desktop. Which I think is what you're meant to do, but I'd still have the same problem. I've tried variations, but to no satisfaction.
I've literally spent days trying to get this to work right.
Eventually I got Groovymame behaving nicely by going back to normal landscape view, and using VMM to generate modes and export settings as though I was going to play everything horizontally. That is, horz monitor, no rotated desktop, aspect 4:3.
Then I used the "irotate" software tool to rotate my desktop to portrait, edited mame.ini to set "orientation vertical" and "aspect 3:4", and Groovymame is now behaving properly, showing vertical games in non-interlaced modes (and doing a very good job of it too, for the most part).
I got the idea from this post in 2016 where someone must have had a similar issue.
I had the same issue. What I did was start from scratch, set everything up as if going horizontal with super resolutions in vmmaker, leave the desktop horizontal. After all that is done and GM is working, go to desktop and rotate, then the final step was in groovymame ini set orientation to vertical and and ratio 3:4. Trying to set up vmmaker with vertical desktop was nothing but headache for hours.
So, I think the reason why it didn't work right for me might be because I didn't install the ATI driver or Catalyst software (or rather I uninstalled it some time ago) before CRT_emudriver - iirc the ATI driver gives you a monitor rotation option that isn't available otherwise. I just installed CRT_emudriver without anything else and used irotate. I suspect that VMM/Groovymame don't properly recognise the rotation via "irotate", which would explain the problems I've been having.
Which I guess means I can keep doing this the way I am, or go back to square one and install the relevant ATI Catalyst for a Radeon X300 card (and re-install CRT_emudriver) and use that to rotate the desktop instead.