
First of all sorry for my bad English as this is not my mother tongue. And also sorry if my question has already been raised, yet I couldn't find any similar thread when searching with key words...

I'm facing a very weird problem.
I am using the Motu MicroLite as an interface between my organ console and the virtual organ software Hauptwerk. For those not knowing it, it's quite simple - each time I'm playing a note on the organ, it sends a MIDI signal which tells Hauptwerk which note to play with which registration.
When playing, I used to be reading the music sheet on MusicReader (MIDI de-activated as not needed).
Recently I tried to upgrade from OS X 10.10 to OSX 10.11 El Capitan. All went fine, excepted the MIDI flow. When I tried to read the music sheets - meaning the focus was on MusicReader - it was fine for a few minutes, then the audio was stuck. Nothing could be played any longer, despite the MicroLite was still working - flashing when a key or whatever part of the organ was depressed - but no sound coming from Hauptwerk. When bringing back Hauptwerk in focus, all the stuck instructions were instantaneously released and I could go on till the next issue.
I tried to contact MusicReader support, which on the basis of the activity logs concluded nothing was wrong with their software. Same for Hauptwerk. I tried to download the Motu USB/MIDI new drivers (Feb. '16). No success.
I tried then to come back to Yosemite through the Time Machine. Success for the process, failure to solve the issue. Tried several workarounds (including but not limited to activating MIDI on MusicReader, restricting MIDI on Hauptwerk, etc...), still no success.
I then tried to upgrade to El Capitan again. No more success. And this time I coudn't come back to Yosemite, the process hung at the very end of the it. I re-installed the Mini completely from scrap - clean installation of Yosemite from a version downloaded on the App Store. Re-installation of Hauptwerk, the instruments, MusicReader.
It came even worse. Before I could play without MIDI issue if other apps rather than MusicReader were in focus - tried with Reaper, Garage Band, Preview, etc... which were fine. Now, if Hauptwerk is not in focus, and even if no other app is running, it will simply do not work.
I completely fail to understand what is the issue. I don't know what to try next...

Does any one has an idea of where the problem could come from, and how to solve it?

Thanks in advance for all suggestion / comment / other...
