Looks like you might be hitting
Bug 8711 - Custom Zimlets not found after upgrade
I've seen this a lot, in particular on RC1 and RC2, but we think we have it fixed now.
In the interm, undeploy all your zimlets.
Then, go to /opt/zimbra/tomcat/webapps/service/zimlet
and remove the files for each of the zimlets you have removed.
Then stop zimbra
cd /opt/zimbra/tomcat/work
rm -rf *
start zimbra and redeploy