Welcome to the forums,
Not a perfect solution, but in the interim you could:
Backup the /opt/zimbra/bin/zmantivirusctl file
As the zimbra user create /opt/zimbra/log/clamd.pid.fake
Then as root, in /opt/zimbra/bin/zmantivirusctl right after the line:
/opt/zimbra/bin/$i start norewrite
So that everytime clamav starts it creates the clamd.pid file from clamd.pid.fake
cp /opt/zimbra/log/clamd.pid.fake /opt/zimbra/log/clamd.pid
-Be sure to check for running processes anytime you stop zimbra (ps aux | grep zimbra).
When you have the time, some things to try:
1) zmcontrol stop and check the /tmp for any entries relevant to clamav that may need cleaning out.
2) I know you just updated clamav but to clear the defs anyway:
3) Make the jump to 5.0.2: http://www.zimbra.com/forums/announc...-released.html
su - zimbra
mv /opt/zimbra/clamav/db/* /tmp/clamdb
zmprov ms `zmhostname` +zimbraServiceEnabled antivirus
4) Besides your excerpt from zmmtaconfig.log, anything in clamd.log?
5) Start a support ticket so we can have a look