I just had the same problem
first my doc would disappear and only show up when I had the mouse over it
I checked preferences - Automatically Hide and Show the Dock was unchecked
I checked it.. then unchecked it...
so now the dock stays visible
but Mail disappeared
I opened the program... then left clicked and said KEEP in DOCK
now it is gone again
... the Dock seems to have some new *features* hope Apple fixes them as some would call them bugs!