Not sure if this can’t be changed via the Devices setup. It might also simply be embedded in the template if you start from those. (?) Make your own template, change from All midi inputs and then save out. I’m still not sure what would cause your stuck notes. I’ve got a basic idea why but that’s about all I can be sure of not being a specialist engineer and also being remote. Usually a stuck note is caused by an OFF note not getting there or passing thru at the same time (just before) as another ON note I’d check your midi channels and see if any are addressing two instruments somehow (an on note from instrument A overlaying an off note to instrument B). This could be caused by everything going thru All midi inputs instead of dedicated inputs.
The midi filters are on by default as an old rule from the Atari to save on resources. Time to change that maybe.
I’m offski. Happy Christmas and New Year all.
I just solved this issue by making sure that both the Direct Music and Windows MIDI were not checked as in the MIDI settings (F12) as part of the “In All MIDI Inputs” column. That did the trick!
‘All MIDI Inputs’ just means any input from any MIDI device, [keyboards, V-drums], and any of the 16 MIDI channels.
[In my case, I use 2 keyboards, a V-Drum brain & a MIDI sequencer that feed into Cubase.]
Very convenient.
Saves from having to assign a particular channel & keyboard if you don’t want to.
There was a post on here that I read just the other day, and I’m sure the OP found out that his Axiom 49 was the culprit for his nightmares.
Have a look for that one and see if it has any similarities or suggestions that might help you.
most troubles turn out to be “PICNIC” troubles. there are several very good cubase tutorial videos available that cover quite a bit from “midi reset” to "setting up a midi track (input/output, etc) and many more advanced features. even a seasoned vetran can use a refresher occassionally 
The problem is caused by the shitty drivers for the M-Audio. They don’t work properly in Vista/7 or 8/8.1.
I had the same problem so I got rid of it and bought another MIDI keyboard - and all my MIDI hanging notes/other MIDI issues/problems were gone. 