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[RDC]

The media remote is IR, the controllers are RF, they don't have anything to do with each other so one working and the other not doesn't really mean anything. The PnC cable does not make the Wireless controller Wired either, it still connects via RF and only forces the controller to sync to the 360, provided the RF of the console works properly. Replace the RF (RoL) board, that should be all that's wrong with it, unless you damaged something the last time it was apart. If you have another 360 to swap RF boards you'll be able to tell right quickly if that's it or not before getting a new one.

[RDC]

The Wired controllers also really have nothing to do with the Wireless ones, except where the signals end up at the Southbridge.

Remotes are IR

Wired Controllers use USB ports

Wireless Controllers use the RF board

Replacing the RF board should get you all sorted. More than a few people around here have had it up and 'die' on them from taking the console apart and then just putting it back together.