I have this problem with some packages, in particular open-recent and build. For some reason they don’t save their settings.
For example, open-recent should save a list of recently open files and folders but the list is always empty. It doesn’t remember the maximum number of list entries that I set, although I can see the correct number in package preferences. Build should save the height of the build window but next time I start Atom it always goes back to default, and again package preferences contain the right value.
I checked my ~/.atom directory to make sure everything is writeable. I also deleted the whole folder and installed the above packages again - no luck.