Hey mate, from what I've read this is a pretty common problem with the Genesis, due its age. The problem is quite often the solder joints on the pins of the port, that connect it to the main board are cracked/broken. This is due to people yanking the controller to disconnect it and ramming it back in, over and over. Luckily, if this is the cause, all you need to do is, open up the Genesis and reflow the solder joints.
This guide should help you opening your Genesis up, and getting the main board out; Sega Genesis Motherboard Replacement
And this should tell you how to reflow the joints (ok its using an amp, but its the same process); Reflowing solder joints on a TEAC GSA-5300 stereo integrated amplifier
Hope it helps you
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