Are you using local file storage for anything such as storing session data? Heroku's file system is ephemeral which means you can't rely on any data that's not part of your original codebase to stick around between deploys.

My guess is that's the root of your problem as I can't think of anything else that would cause this issue. I use Heroku for all of my sites (including WIP) and never had this problem of users being signed out.