If the O2 circuit fails, then that may be how the PCM compensates; but if the circuit is good then the PCM will trust whatever the O2 sensor is telling it, including if the O2 sensor falsely reports a rich condition. I've seen it happen.
If the O2 sensors are not in the stock locations, then yes, it's also possible that you'll need to change the appropriate sections in the BIN. That being said, was this something it always did since the swap (and/or the moving of the O2 sensors) or did this just suddenly happen for no apparent reason? That should help narrow things down.
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