Changes have been made in Git (master):

commit 634eabbe80f77c814acd8d21fb14c6b7f20a4a9a
Author: Jan Schneider <jan@horde.org>
Date:   Thu Jan 24 15:58:00 2013 +0100

     Fix unselecting all custom alarm notifications (Bug #11879).

  kronolith/lib/Event.php |    4 ++--
  1 files changed, 2 insertions(+), 2 deletions(-)

http://git.horde.org/horde-git/-/commit/634eabbe80f77c814acd8d21fb14c6b7f20a4a9a

No. If I uncheck the checkbox, then save it and reopen it, the 
checkbox is still unselected.

Question about this step:  Do you explicitly click on the "as default" 
radio button?
This works for me. Just unchecking the checkbox is not enough to reset it.

I can't reproduce this, though I'm not sure I completely followed your 
report. What I did:

Dynamic view:

Create new event
Add a custom notification with email
Save
Reopen
Remove email checkbox from notification
Save
This correctly removes the email notification when I look at the event 
again. I also tried this with a number of other combinations of 
notification methods.

Did similar tests in the basic view as well.

Hi,

create an event with a custom alarm setting. Enable f.e. notification 
via email.
Save the event and re-open it. Now disable the email notification.

-> kronolith does not save the disabled custom notification.
Happens with the SQL and Kolab backend.

Cheers,
Thomas