For this issue to occur, multiple logged in users are required. User number 1 alters a recurrence which contains only one event, and choses "This event only". The shift in question will disapear from the second client (but will still be visible if a third client logs in). If the second client then does any update to the schedule, the shift which had originally been modified by user number 1 will be stripped of all its breaks.
Only have 1 logged in user at any given time.
you can download the fix here:
KB205
This HotFix must be applied 5.1 SP3.
Double-click the HotFix executable and follow the on-screen instructions. This fix must be applied to the server.