Problem with the fullscreen setting in Mountain lion

Hi, I am experiencing a problem with the full screen setting of my Mountain Lion. The trouble is that when I run certain apps such as Zotero or Scrivener and I open, say, the preferences window, this is automatically set in fullscreen, although it should not be so. I have already got in contact with the Scrivener team and they suggested that was a problem related to one of the apps I use to manage my windows, i.e. RIghtzoom and Window Tidy. Following up this suggestion I uninstalled and restarted my laptop, but nothing has changed. I wonder if anyone has already experienced this problem or if you have any suggestions. Thanks.
Alfredo

Not too sure, can you change the Fullscreen setting off in preferences? Are you certain there is no "Save preferences" icon because if you're switching the settings and just quitting, you may not be doing anything,

May just be a software preset?

Hopefully this helps..