You have to look under Processes. Applications only shows the main windows thread, which is gone. It is background tasks (notably the poster or central count) that cause the problem.
Woah... Back up here. Are you saying you can you cause GEMS to crash by printing reports while running central count? Can you reproduce this? Has this been reported? This is serious and needs to be tracked down.
You will almost certainly find a GEMS thread under Processes. Kill it and you won't get the GEMS already open error when you restart. But we need to track down and fix the crash.