Success! Ok i figured it out. This is going to be a long one so sit back, but anyone with a similar problem, i hope this will work for you. Again I am running RetroPie on a raspberry Pi 3 with a Pi2Jamma adaptor and i ran the retropiergb mod to output to a 15khz monitor. so i figured that this was an issue with the run command, so i found a file in the /opt.retropie/configs/all, named runcommand-onend.sh . In it there is a line for HDMI timings that was different then the one in the global config.txt in the boot folder. so i added the correct timings and # out the originals and it worked! but then for some reason mame was outputting a very stretched image at 1920x240, so i went into the configuration options in the run command menu and changed the settings in the edit custom retroarch config option. In it you will see that the custom viewport is set to 1920x240, so i just added a pond symbol before the commands. Since the layout seems to be UK it is a £ instead of # for us Americans but it works just the same. and now mame defaults to the listed game resolution. I have no Idea why these options did this but I wasn't going to let this beat me. I hope this helps.
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