This has happened to four of our players since 1.10, three of which since 1.11, where we had 2-5 players online and another player was on for hours thinking no one else was online and when asked if they were online they said, yes, but couldn't see anyone online, when in reality there were 2-5 online.  The player what was not seeing anyone online, logged out and logged back in again, then it showed them join our session, but they had none of the progression save that they had done for their time played while "being on the realm".

In short, it seems players join another instance of the live realm, but aren't really on a version that is being saved by the realm.