Eclipse: Job found still running after platform shutdown.

There are 3 things to be borne in mind when working with Eclipse:

1) Eclipse is a piece of crap
2) Eclipse is a major piece of crap
3) Eclipse is a disgustingly fetid stinking piece of crap

Having said that, when you encounter this message "Job found still running after platform shutdown", just shutdown everything, rename your .metadata directory in the workspace and restart anew.
Remember also that Eclipse brilliantly writes its log into a .log file (invisible in Linux).... there you will find the real reason for the crash, which of course has NOTHING to do with the error message you get.