Could you post your zmsetup.log.####
do some stop/starts
zmcontrol stop
zmcontrol start
and post the relevant sections of these: (put them in a txt file it's not a huge post)
/var/log/zimbra.log
/opt/zimbra/log/mailbox.log
/opt/zimbra/tomcat/logs/catalina.out
other log files of note:
/docs/ne/latest/administration_guide/9_Monitoring.12.1.html#1075561