I suspect something on your system is grabbing the ports, and that the drivers your controller uses are in exclusive mode (meaning only one app at a time can use them). Some USB/MIDI drivers have flags you can change in the Windows device control panel (enable/disable the exclusive mode), while some are pretty much hard set to exclusive mode.
So…check that if you can. Make sure you do NOT have anything running on startup that grabs the MIDI hardware for some reason. It may be that some motherboards ship with sound studios that are grabbing the ports! I once had a gaming motherboard that shipped with all kinds of fancy junk for gaming that conflicts like crazy with my pro-audio kit. I ultimately ended up uninstalling all the fancy stuff that came with the motherboard and just letting it grab whatever default drivers come from the Microsoft servers (without the fancy extra control panels and game enhancing wizbang stuff included in the box).
Not sure if this helps, but I have some AKAI gear that uses drivers that go into exclusive mode…meaning the first app that grabs them can get access, but nothing else can.
My Roland XR and M-Audio Delta 1010 do not suffer from this. I can run pretty much any DAW I have in any order and all of them can see their MIDI ports and use them at any time (even sending/receiving the merged data over them simultaneously).
My solution if I know I’ll be needing the AKAI MPK261 or AKAI EWI Wind Controller with multiple apps running in the same work session is to use something like Bidule or Bome Translator and virtual ports to reroute the MPK MIDI where I want it to go.
For me it works kinda like this:
First I launch an instance of Bidule that is pretty much dedicated to MIDI routing/echoing/merging/translating. I have it set up to take control of the AKAI kit with the problem drivers. I have to remember to launch Bidule first, or my controllers are STUCK with which ever DAW I run first.
Some of them (Plogue Engine stuff) will not touch the AKAI USB/MIDI drivers unless they are connected to a track/stave or something, while others (Dorico and Cubase Pro), by default, grab everything MIDI it can find in the system on launch, and never lets go until the app is closed (even if not assigned to any tracks, Generic Controllers, Quick Controls, etc.)!
Not only does this help me with exclusive mode USB/MIDI driver(s), it allows me to live-invert a couple of stomp switch pedals I have that are wired backwards from what the AKAI is normally compatible with for the ports I have them plugged into (firmware of the MPK2 doesn’t have a way to switch this built in unless I use the continuous foot controller port, and I actually have a continuous foot controller there! So…to use my nice Yamaha stomp pedals [closed switch when up, open switch when down], I just invert those CCs in Bidule before sending to a DAW). Bidule also has OSC server/client capabilities, so I can set up some Android tablet apps to become MIDI controllers for DAWs that don’t have OSC capabilities built in here as well. All in all, it’s like Cubase MIDI insert power many times over…well before data from the controller even meets the target DAW.
I typically keep several virtual ports loaded and ready to go. I’m on Windows, and like loopMIDI and/or rtpMIDI (if doing MIDI over LAN/WAN) for their versatility in having multiple ports, being able to name them, add or remove as needed dynamically, etc. I’ll use one of those to get this controller data routed from Bidule into Cubase, Dorico, Finale, Sibelius, Etc.
So the routing is MIDI Controller(s) > Bidule > loopMIDI port(s) > DAW(s)
For a long time I was using that first instance of Bidule purely for MIDI, but these days I’m experimenting with ASIOLink Pro, so I’m doing more audio routing and pre-processing from that initial Bidule instance as well these days. It’s pretty cool being able to patch almost any app’s audio (even the non ASIO ones) and MIDI into the Cubase mixer and vice verse