Stuck notes in Mainstage

Buffer sizes, etc are all audio settings. There is nothing to do for MIDI and without more details about your specific case, there is not much that can be said. It must be some kind of edge case otherwise this would be way more common. The problem can be in several places:

• MainStage
• a 3rd party Audio Unit, if used (do you use one?)
• the actual hardware, which might behave slightly weird and the problem just doesn't show up in GB.

Never heard of this, besides broken MIDI hardware or 3rd party problems.