Since we are not running multiple zimbra instances on the same vserver host, it made sense to simply exclude the entire /opt/zimbra directory from hashify. We could have excluded /opt/zimbra/db/data (and I suppose /opt/zimbra/logger/db/data) only but this seemed to kill two birds with one stone (eliminate useless hashification and solve our problem).
To do this, we did:
This assumes a 64 bit system and a vserver named zimbra.
cp /usr/lib64/util-vserver/defaults/vunify-exclude /etc/vservers/zimbra/apps/vunify/exclude
echo /opt/zimbra >> /etc/vservers/zimbra/apps/vunify/exclude
vserver zimbra hashify
There were several other instances we encountered to enable zimbra to run with all features enabled on a vserver although this was certainly the most serious. We also encountered some small issues with CentOS 5.3 We will pull all those together into a how-to for both the Zimbra and VServer communities.
We have elected to not find why hashify and mysql/innodb do not get along. This does not normally manifest itself because MySQL defaults its data directory to /var and /var is excluded from hashify by default. Zimbra's use of /opt/zimbra to store the databases unearthed the problem.
Hope this helps someone else! - John