Here's a workaround that seems to work for me. Use at your own risk.
Add this to the bottom of your .gnomerc:
[ -n "$GNOMERC_LOADED" ] && return
GNOMERC_LOADED=1
((
TIMEOUT=10
IS_XSESSION=`echo $0 | grep -c Xsession`
BLACKLIST_DIR="$HOME/.config/indicators/messages/applications-blacklist"
PS=0
if [ "$IS_XSESSION" -gt 0 -a -d "$BLACKLIST_DIR" ]; then
while [ "$PS" -lt 1 -a "$TIMEOUT" -gt 0 ]; do
PS=`ps -u $USER -o cmd | grep -v grep | grep -c indicator-applet`
TIMEOUT=$(($TIMEOUT-1))
sleep 1
done
BLACKLIST_TMP=`mktemp -d`
if [ -d "$BLACKLIST_TMP" -a -n "`ls $BLACKLIST_DIR`" ]; then
chmod 700 $BLACKLIST_TMP
mv "$BLACKLIST_DIR"/* "$BLACKLIST_TMP"
mv "$BLACKLIST_TMP"/* "$BLACKLIST_DIR"
rmdir "$BLACKLIST_TMP"
fi
fi
)&)
--
indicator-applet forgets blacklist for messaging menu after restart
https://bugs.launchpad.net/bugs/538427
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