Benny, what you should do is place the MFX loco on a track connected to an MS1 via the ugly box and let the MFX do the registering process.
Once it will be registered with the MS1, you can put it back on the CS1 Reloaded connected track and the registering process will start all over again for this controller, MFX locos have never been into the database.

The situation is a mutual agreement (or mis-agreement) between the CS and the mFX decoder.

During the original registration process the CS polls for new devices by including its own controller ID as part of the message.
When the decoder receives such an "anybody new?" poll coming from a Controller ID "he has not heard from before" it will respond and initiate a communication to pass details about itself. If the decoder already knows of the ID and believes that it has already told the CS about itself, it will ignore subseqent polls.

So in answer to your question.. No it is not so much the CS setup that has been overlooked, but the clearing of the decoders memory.

The suggestion to directly connect your MS is aimed at causing the decoder to "replace" the controller ID it has a memory of, with a new one. Once this has been done then, theoretically, placing it back within the CS domain will cause it to think that the CS is a new controller and it will participate in the (re)registration process.

My suggestions
0) Double check that you have really deleted all references of the item in the CS. Consider if you may have used the loco in a consist.
1) with the MS - perform a change (rather than just do the registration) - e.g. add a letter to the name and write it back to the decoder.
1a) Maybe try - "reset to factory defaults"
2) try placing loco on the CS programing track (with nothing else to cause confusion)
3) WAIT - the CS registration can take up to 30 seconds to start and then another 2 minutes to complete
4) Reset the CS to factory defaults.

Note: Even before registration , if the decoder detects that the layout it is on is controlled by a different controller, one of the first things it should do is "stop" (bit of a safety feature). If you use the MS to set the loco moving at a slow speed, press MS stop, place loco on CS track, press CS GO - you should see the loco move forward for a short distance and then stop. While this may not be 100% reliable it may give an indication that some sort of recognition is taking place.

Summary: The symptom you describe is becoming less frequent, possibly newer decoders and CS code updates are better at handling it, but still crops up.

Hi Peter, thanks for this explanation, now I understand this whole issue much better.

I followed steps 0 though 3 plus the note. The CS and the decoder simply ignored each other.

I had hesitated to perform step 4, as I would loose all my other loco settings, but with nogo with all the previous steps, I finally did reset the CS.

I lost all data, but the registration process initiated. The M4 symbol showed up in both sides and after a while the BR64 was ready to go. :-)

Thanks again, it was a relief, that my BR 64 was back in business, lonesome though as most of my stuff is stored away anyway, only a small test circle on the floor and a few recently eBay acquired locos to run. :-(

Nice trick, Nev. Is there a logical explanation to this ?.
I will try and remember for a next time.