Try the settings from command line, e.g.
groovymame bublbobl -nofilter -nounevenstretch -nounevenstretchx
That should work. If it does, put those settings inside an .ini file other than mame.ini, e.g. raster.ini, horizont.ini, vertical.ini, etc.
Some settings in mame.ini can be bypassed by Switchres to allow automatic configuration. When they're set somewhere else, they get higher priority and GM can't touch them.