As you've found out, Logic puts all MIDI data for one Track into one Region, whereas Cubase uses several Regions if it thinks its beneficial. This does not affect playback and does not matter, as there are no Regions in a MiDI file anyway.
But this is not the cause of your problem.
Arranger keyboards are notoriously finicky in combination with a DAW, they are specifcally designed to not require a computer, and this often goes against compatibility.
It seems there is something in a Logic MIDI file which isn't in a Cubase MIDI file of the same music, which irritates your keyboard. Upload two versions and we may have a look. Narrow it down to the simplest file, maybe even without any notes, which still triggers the error.
Also, it would help tremendously if you would tell the specific error message.