If delivered mail doesn't show in user inbox

One of our Ubuntu servers stopped to show properly delivered messages in user inboxes after the last kernel update (Ubuntu precise (12.04.4 LTS)). Because for some reasons DEFAULT= and ORGMAIL= in /etc/procmailrc got replaced by

DEFAULT=/var/mail/$LOGNAME
ORGMAIL=/var/mail/$LOGNAME

so we had to change it back to:

DEFAULT=$HOME/Maildir/
ORGMAIL=$HOME/Maildir/

Now everything is working fine with the following settings for procmail:

root@quiethost:/etc# cat procmailrc
LOGFILE=/var/log/procmail.log
TRAP=/etc/webmin/virtual-server/procmail-logger.pl
:0wi
VIRTUALMIN=|/etc/webmin/virtual-server/lookup-domain.pl $LOGNAME
EXITCODE=$?
:0
* ?/usr/bin/test "$EXITCODE" = "73"
/dev/null
EXITCODE=0
:0
* ?/usr/bin/test "$VIRTUALMIN" != ""
{
INCLUDERC=/etc/webmin/virtual-server/procmail/$VIRTUALMIN
}
DEFAULT=$HOME/Maildir/
ORGMAIL=$HOME/Maildir/
DROPPRIVS=yes
:0
$DEFAULT