When one is typing a note in the Message Notes section, if one types a keystroke like 's' (which is used for saving a message), or 'c' (for copy a message), the focus changes from the Notes to the Nostalgy function.
I'm not sure if this would be an issue to address from Message Notes Plus or Nostalgy (or both), but I thought to let you know as Nostalgy is used by a quite a few users.
As I see from the Nostalgy's code it catches any key presses in the main Thunderbird window. This is quite aggressive behavior. By example, Thunderbird's native hotkeys, such as F,G,A,... work well with MNP.
The most appropriate way to fix this incompatibility is to change Nostalgy's code. Let's see if anybody else wants to use MNP with Nostalgy together.