I'd say it depends on what RF receiver was actually fitted as the replacement. If it was a Gen3 receiver, then yes, a bit of a head scratcher, but there are a couple of explanations I can think of.
If it's a Gen2 receiver that a previous owner bought because it was 'upgraded' then it's still prone to interference (but not as bad) and I've heard that the interference to the BECM will cause all sorts of strange things with EKA etc. I am guessing that the RF receiver data works on an interrupt to the code in the BECM CPU - so that when a transmission from the FOB is received, the BECM then does the number crunching on it processes lock/unlock commands if they are valid. My best guess is that if there is interference then on Gen2 receivers, this will then end up on the data line to the BECM which will then interrupt what it's currently trying to do - eg listen for the EKA.
It could also be the passive immobiliser is still turned on and it re-immobilised the vehicle, and then the mobilisation code from the fob wasn't able to be received due to the interference, so then it would just sit there and ask for the code.
Either way, I would at some point be testing the door latch microswitches, as if one of them is faulty/intermittent, then that also won't help matters!