Well, I played the game to the end of the first mission. I even did the Romulan encounter after saving the doctor on the planet. I didn't get any glitches during any of that.
As far as I know, my rom is a verified good rom, which also means it has no intro. I would suggest that you get a tool to check your rom to see if it;s a good rom, and make sure your running the latest version of Hakchi2. There may have been a change to the way the game gets added that can fix any bugs that you get.
I'm pretty sure that no-intro and good roms are two different things... No-intro's requirements are more stringent than Goodroms...
They are two different standards... No-intro has the most stringent standards.
https://www.reddit.com/r/emulation/comments/3ewr2t/goodsets_vs_nointro_roms/
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Super Gameboy Support does work I will get a video up of how to do it by tomorrow I got it going awhile ago.
Can't wait to see this!