If you put the programme into mode 3, notes mode, and place some notes on arbitrarily chosen residues the notes will not be there when you look at them later.
This has happened to me 3 times, but I am unable to determine at which point the notes are lost - since you only find out they are gone when you need to look at them again. When first typed in, they appear on the screen as they should do. If you switch out of mode 3 and then back into it, they will still be there but then dissapear at some point down the line.
Hope you can find the bug,