I had the same problem once, although with controller port 2. What had happened with me is someone had jammed the controller into the port too hard and actually jarred the board inside loose. When I would plug in the controller, it fit ok but wasn't making a good connection inside the machine.
This could also be caused by repeat plugging/unplugging or if a controller was pulled out by someone tripping over a cable or something. I wouldn't recommend opening the system yourself as it will void your warranty, but if this is the issue, it is very easy to fix.
Another possible problem is just a bad controller, try another controller if you have one, if not, plug your current one into port 2.
you may need to change the port station. they could be malfunctioning or the cable that goes to it, may be broken. you can order these parts or send it in to get fixed. it is not a big problem.
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