Use a midi interpreter like MidiOx to see what is happening.
As I said I am sure I use s3 between Miniak and BCR2000 so.that messages from Miniak update BCR display and vice versa.
I rarely use the learn functions. Typically i read the sysex in manual - Miniak was different - AKAI didn't supply it!
Sometimes there are.modes on the synth that stop.it send messages..other times the synth can send real.time clock messages that prevent learn working well.
Mark's BCR manager is a must IMHO. You can edit and layout panel much easier than official tool.
The other thing to consider ....have you looked at Ctrlr? I used this to write panels for Kawai K1r and K4. It's pretty good on Mac, PC or Linux
It appears, using Mode S4, that I got MKS50.syx (from this group) loaded into a Preset on my BCR2000. That's great. Unforutnately no response from the MKS50.
I have the BCR and MKS, and my control keyboard, all connected to my MIDI patchbay with the control keyboard and BCM merged into the MKS. The MKS MIDI indicator flashes and the synth plays sound in response to they keyboard but doesn't do anything when I turn knobs on the BCR. The BCR shows red LED activity on MIDI OUT A when I move knobs.
MIDI Exclusive is on in the patch (on the MKS) I am trying to modify via the BCR.
Any ideas?