When I shutdown my minecraft it never closes all the way, I have looked for a solution but found none. After awhile I gave up and decided that I would manually kill it when I wanted to close it.
If I use pgrep then kill in the terminal it seems to have no affect, but when I open the system monitor and right click and kill it, it shuts down nicely.
What are the differences between the System Monitor way and the Terminal way? Does the System Monitor do something else in the background that the kill command does not?