Hi Matyas,
Have you tried all methods of killing the notes application? I have no familiarity with Notes Basic but here's the few ways I know of to try kill an application to test out and see if you get different results.
A) Try killing it with a Navigate stage in an object for that application
B) use the Utility - Kill Process Action and give it a list of all known processes that Basic Notes uses and kill them until Blueprism can't see them anymore
C) Try making an object to click on the 'x' at the top of the application
D) try making a batch file that Blueprism can execute externally from it's running behaviour
E) try making a VB Script that will kill a process after 'x' seconds/minutes
F) try it manually, interact with your application in debug mode and then terminate Basic Notes manually and if that causes Blueprism to not shutdown ten you know it's possible to terminate the application without affecting Blueprism
I have never heard of Zap Notes and Killnotes, so I presume they are objects you have internal on your own system. Might be worth your time exploring them and seeing exactly what they do to understand why BP is shutting down also.