I have come across a possible workaround that is working in my environment.
In the document properties/variables tab, for each of the user variables i have ticked the box for “Include in Bookmarks”. After several document reloads using publisher the variable values are being retained after each refresh. I was having a similar issue with Date variables changing back to defaults and now it appears fixed.
Note: You need to reload it a first time, then change your variables and reload again to see the changes is working.