I had the same issue not that long ago, and it turned out to be a clash with
Acrobat 7 and 8, Do you have either of these?
If so I shall post the solution below.
But in the mean time you can use Shft+File, and use SaveAll. This does
ensures the new Auto Entries are saved. Do this work for you?
I followed the following instructions:
http://www.gmayor.com/lose_that_adobe_acrobat_toolbar.htm.
but also found that after I did this, reboot, then I reinstalled the
Acrobat, and all is working fine now.
Hope this helps
DeanH