Probably doesn't have to do with your issue, but upon reading your post, I remembered this little bit of trivia about the centering of the arcade controls (from Atari hardware engineer Jed Margolin's site- http://www.jmargolin.com):
"You might have noticed that the centering of the Star Wars control yoke is funny at times. Star Wars originally used a Pokey to read the pots. At that time, people either made their own A/D converter with a counter, a comparator, and a ramp, or they used Pokey. The Pokey was a full custom IC designed for the Atari 800/400 to read pots and keys, which gave it its name, POts and KEYs. There was some room left over so they put in some crude square wave sound generators as well as a UART. Unfortunately, Pokey does a really awful job of reading pots; it is guaranteed to produce occasional wrong values. The software to deal with it is pretty nasty. After Greg Rivera brought this to my attention I took the daring step of actually putting in a real A/D (Gasp!), the ADC-0809. Unfortunately, many people continued to use the original code to treat the A/D values as though they had come from a Pokey. Like Greg. That is why the Controller in Star Wars keeps getting recentered, usually badly."
"One of these days, I'm going to cut you into little pieces!"- Nick Mason, Pink Floyd
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