for the license issue:
try just copying the licence file in your filesystem and rebooting-someone else had that issue on upgrade (there's a thread somewhere)
Reinstalling all the zimlets fixed the problem.
I copied out all the files in /opt/zimbra/zimlets and /opt/zimbra/zimlets-network to /tmp/zimlets/. Then for each zimlet I ran:
zmzimletctl install /tmp/zimlets/[zmlet file name]
Restarted tomcat and all was back to normal.
Thanks for your help.