I am experiencing this same issue, as are other players on my (Java) realm. In several cases, someone hsa logged on, played for two hours, then logged off. Then when logging on the next time, they find that the server acts as if that entire two hour play session never occurred.
What Shane Sanders above describes is the same issuing occurring on my Realm. Several people have played for over an hour or two, logged out normally (no crash, not getting kicked), and when they log back on next play session, everything they've done has not been saved, as if their previous play session never occurred. Anecdotally, this seems to be more likely when only one person is on, though on at least one occasion, another player logged on, did some stuff, logged out, and logged in later to find all her progress nonexistent, while I was online the whole time and unaffected.