...it seems it happens when you stop the Mac manually or with power save instead of shutting of it.
Really annoying.
What do you mean by "when top the Mac manually or with power save"? Do you have the problem when the Mac is going to Sleep and not when you shut it down? or the opposite?
Did you try without MOTU device connected?
Hope you can solve this issues because I'm waiting 3 Elyseum AL-88c to configure and all this seems to became a really mess.
Sure, I understand your concern! But I need more feedback to understand what is occurring. And first of all I would like to know if the issue is still there when you are using exclusively CopperLan software/devices, because it could be a compatibility issue with other things (in this case your MOTU equipment).
About your Novation keyboard connected to the iMac: if you want to control Pro Tools running in your Mac Pro from this keyboard connected to your iMac, you have first to ensure that the keyboard is handled by CopperLan (CopperLan manager/Edit tab/MIDI on iMac/MIDI to CP/{your keyboard}: turn it on), then go to the CopperLan manager/Connection tab, select MIDI on iMac/{your keyboard} and create a virtual MIDI cable to some port of the Mac Pro (VMIDI1 for example). Finally, set up Pro Tool on the Mac Pro to listen to the port used as MIDI cable target. If Pro Tools is creating itself some virtual MIDI port, you can also handle them in CopperLan (same procedure than for the keyboard, turn on Edit tab/MIDI on Mac Pro/CP to MIDI/{pro tools port}) and then you can directly connect the keyboard's CopperLan endpoint to the Pro Tools CopperLan endpoint. Quite hard to explain without drawing support
Let me know if it is not clear for you.