That seems odd. Possibly a bug with groovymame?
I don't remember the details off the top of my head but, depending on your settings, mame will/may write to a config file to the CFG folder and an ini to the INI folder. You might try deleting the cfg and ini files for that particular game (if either exists) and then see if the mame.ini will take affect. I doubt it is part of the issue, but I'd also delete the folder for the game under the NVRAM folder, just for grins. Also,
You might also try a fresh install of both groovymame and "regular" mame and see if the problem still happens in either.
Good luck!