I've had this issue with every recent version of PSE.
I'm using 64 bit Windows 7.
When I close the organizer, the "Elements 12 Organizer" process is left running.
This prevents PSE 12 restarting, without me manually killing the process from the task manager. I have created a shortcut to the organizer, as I know using the launcher has had issues in the past. I had a forum entry from December 2012 for the same problem with PSE11 which went away when I stopped auto-analyzer in the preferences. This seems to make no difference with PSE 12, which runs "ElementsAutoAnalyzer" anyway!
If I kill AutoAnalyzer process it also makes no difference to PSE 12 Organizer restart.
You might have a look at this solution:
Killing that process has solved for me the problem of saved files not included in the organizer.