There is a menu glitch on the SNES console in your arcade. The first page of games works fine, but the rest of the pages are still secretly the first page. So for example, if you scroll to the third page and pick the 5th game down, it will choose the 5th game on first page. If you choose the 6th game down, it will play the 6th game from the first page. Whatever you choose, it will play whatever game was in that slot on the first page.
So the workaround would be to only keep one page of games in the folder at a time. But it would be cool if this were fixed.