My Krustyburder Hideouts are also resetting every time I quit or go to Krustyland or the Neighborhood. But only in 2 of my games. In my third game the timer is working correctly.
My first 2 games are level 59 with 3 Krustyburgers each. My 3rd game is level 46 with only one Krustyburger.
I tried storing the additional Krustyburgers in game A, but that didn't fix it.
I haven't had any problem with my characters getting stuck in any of my games though.
I've reported this issue to Customer Support
http://help.ea.com/ , but the more people who report it the sooner they'll get it fixed.
When setting up the case with support select "Technical support" as the Topic and "Game performance" as the Issue to get to a service representative.