Product Version = NetBeans IDE Dev (Build 20110711-19a9d9a0205b)
Operating System = Linux version 2.6.37.6-0.5-desktop running on amd64
Java; VM; Vendor = 1.6.0_26
Runtime = Java HotSpot(TM) 64-Bit Server VM 20.1-b02

Since the fix for #198665 our tests (in versioning) started failing occasionally. After a long digging and debugging NbPreferences' code i came across a probable cause. If i understand correctly, modifying prefs comes in the following steps:
1) value is stored in memory in a map of properties
2) an async task is run after 200 ms that takes the map and persists it on disk in a preferences file
3) at the end of the async task FS fires a fileChanged event that results in calling NbPreferences.stateChanged method that empties the whole property map kept in memory

Now what happens when someone calls NbPreferences.put(...) right between 2) and 3)? Unless i am mistaken, the change is not stored and instead dropped into a black hole. I'll attaching a test demonstrating the problem (but it's an artificial one).
Hard to say if this may affect something other than unit tests, but you should definitely at least know about this.