We have a Windows 2008 server (not R2) acting as a primary file source in a DFS replication group with a single other server that happens to be Windows Storage Server 2008. All is well in terms of 2-way replication.
What we cannot explain is how at random times the replicated folder on the primary location is becoming hidden and system on its attributes. Users call to ask where did their folder go. I've set up a scheduled task that runs every 5 minutes to log the folder attributes to a file so I can nail down a window of time when the attributes are getting flipped. Then I've created custom filters in the Event Viewer to show all events around this time frame (+/- 10 minutes), and checked it on the primary file server, secondary file server, and domain controllers hosting the namespace.
I cannot find a single entry that looks out of the ordinary to explain what's happening. The closest event I can find that occurred on the primary file server and 2 of the domain controllers is a informational Group Policy event (ID 5327) saying "Estimated network bandwidth on one of the connections: 0 kbps." But I'm not sure this is related, and even so on the primary file server a second or two later there's another ID 5327 telling the bandwidth on a connection is back up to normal.