I recently had this happen to my wife's 23 NX. Took it to the dealership on Feb 5th and they found an open circuit in the floor shifter and replaced it. Haven't had an issue since.

To quote the write up: "Open circuit in shifter assembly T1 87 T2 71 FPN#33550-F6012
Verified malfunction indicator would come on intermittently. Found internal open in shifter circuit. Replaced for shifter with updated part."

 

Well let's see if that service bulletin is ever issued - based on the lack of one for the intermittent windshield wiper issue, I am not optimistic they will ever issue a formal one.

 

One more RX affected here. I've seen the Shift System Malfunction error three times now. I'm in North Carolina, so it's not very cold here, but the error does seem to happen after the car has not been driven for several days. It took it to the dealer. They said there is nothing wrong and maybe the "transmission fluid was cold".

 

byzatic: Press the dealer for a software update to the gear control module. It exists, but does not appear to be released. The Lexus regional service manager for CT authorized it to be installed on mine for this problem, and it corrected the issue. Consider asking for the contact information of your regional service manager.