I don't think you should need to use user modes unless you're using other emulators that need specific defined resolutions. The point of super resolutions is that they are generic resolutions that scale horizontally as needed to cover a range of different resolutions. That way you don't need to have a ton of fixed resolutions installed. Windows gets weird when there are too many resolutions. This is why super resolutions were created.
I don't think you ever identified what kind of arcade monitor you are using. When you go through the driver install process, what monitor are you picking?
GroovyMAME should be picking the correct native resolution from the super resolutions except in the cases where it's deemed "more optimal" to run in a higher resolution. For example when you try to run a vertical game on a horizontal monitor, it will usually pick a higher non 15khz resolution (or an interlaced resolution) in order to hit the correct refresh rate.
I think you should run through the install again for super resolutions, making sure to enable EDID emulation, and pick the tri-sync arcade monitor (or the exact model you have if it is listed. Don't install any user modes. Try to follow the steps exactly...
http://geedorah.com/eiusdemmodi/forum/viewtopic.php?pid=1052Then for games that don't work the way that you think they should, generate log files and attach them to a post...
Steps to create a log:
- From command line, run: groovymame.exe -v romname >romname.txt
- Attach resulting romname.txt file to your post, instead or pasting it.
Calamity is generally very good with helping troubleshoot these kinds of issues as long as you post log files.