Hi Phil,
 
thanks a lot for your help!
Your questions helped me narrowing down the problem: it occurs, when a *Org Note* Window open, which lets me enter a note about the change.
This is the case for changing deadlines, but it is not activated for scheduled dates in my configuration.
 
So that means: if I have 3 entries which already have a deadline and I try
* (marking all) Shift-B d
and then choose a date,  I can enter the note for the first entry and indeed there is a message
"Acted on 1 entries, skipped 2 (disappeared before their turn)" in the minibuffer.
 
I found a corresponding bug report - it seems to be fixed (but I installed the stable version):
http://lists.gnu.org/archive/html/emacs-orgmode/2016-03/msg00322.html
 
Kind regards
 
Martin