On OS X, when I stop CDK in JBDS, I get this in the console:
==> default: Unregistering box with vagrant-registration...
==> default: Attempting graceful shutdown of VM...

And a few seconds later, the server adapter shows "Stopped".

Today while testing on Windows I noticed that it behaves differently.
It first displays these two lines, but it keeps "Stopping". And eventually there is another line in the console which says:
==> default: Forcing shutdown of VM...

After this, the server adapter shows "Stopped".

So for some unknown reason, on Windows the graceful shutdown fails to work.

This is JBDS+CDK installed from the latest windows installer (built April 4th).
It would be good to see if others see this on Windows as well or not.

Interestingly, when I just tried "vagrant halt" from cygwin instead of in JBDS, it stops normally - graceful shutdown.