Been experiencing this for awhile and can confirm issue. CB 12.0.40 - On Cubase launch and first file open it will not happen, close file and open another file then issue will happen. Additionally, we found that if we recorded again in this state that the previously recorded midi Part would get erased and Undo wouldn’t get it back.
The Disable/Enable track workaround works. I tried removing external Midi devices (Fadermaster, Stream Deck Midi) but did not help (I have Vienna Instruments, Nektar P4, and Keyboard Maestro in Midi device list). (Side note: I was getting two or three automation lanes randomly popping up on one system, turned out to be Stream Deck Midi, removed that via Stream Deck store and that problem went away).
We use Keyboard Maestro for several Transport functions involving arming and disarming tracks and recording Automation. So we built in the Key Command toggle “Audio - Disable/Enable Track” as well as “Edit - Select None”.