Why do my apps open in a single space when resuming?

When I restart yosemite and I select 'reopen windows when loggin back in' I have a lot of apps that open in the same space. For example when I have sublime text and libreoffice open in a space and restart, the space they they were on will be empty. They will all be on a single space but only in the mission control view and not in the actual space. In contrast to safari and other osx native apps. I would just like to be able to shut down my macbook and resume in the exact same way. Is there a setting for the apps to resume in the space there were on, fully openened?