Hi, I've had the "Not closing down" bug a bit with main release big Gnome LinuxMint, and put it down to lack of available memory to administer the coup de grace on the processes. Have you resolved the problem yet ?
It has been a less frequent, almost non-existent problem with installed LXDE, but then I'm using a big extravagant machine with 384MB of RAM, all of 50% more memory than the minimum recommended. Have you failed to close down an inactive web-browser (Mozilla etc) process, perhaps, before hitting the shutdown menu.
I used to use the "halt" command to shut down LXDE before I worked out how to get the desktop and installation running on the live disk by typing "sudo lxdm" at the terminal command line, and the halts didn't always work then, leaving me with an inaccessible process - nothing to do but press the big red button. The "logout" button gives you a menu containing a choice of quietening down actions, from actual "logout" which leaves the machine unstoppable, to "hibernate"s - which work, and shutdowns, which also work in the available memory.