So it's about to get weirder, I was experiencing many more problems such as hitching and freezing... on a whim, I went into mame.ini and turned off multithreading. All my problems went away. The hitching, the input flickering, all gone. I doubt that that necessarily narrows any of this down, but I thought it would be interesting to report. I have a Core-i7, I figured turning multithreading on would be an improvement. Then I saw a discussion about it on the forum in arcadecontrols.com... So I'll be leaving it off from now on.
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