Its actually in the /etc/init.d/snort file and this is where it appears to fail:
case "$1" in
start)
echo "Starting Intrusion Database System: SNORT"
$SNORT_PATH/snort -c $CONFIG -i $IFACE -g $SNORT_GID $OPTIONS
if [ "`pidof $SNORT_PATH/snort`" ]; then
echo "SNORT is up and running!"
else
exit 0
The problem appears to be related to last time I pushed out the rules and update made changes to some regular rules files, emerging threats rules and to a couple of the configuration files. If I set to rule path to an old directory with older rules and configuration files it works fine. I have posted this as well at snort.org forums but posted it here as well in case anyone else had seen similar issues after updating via policy manager.