Ok, I think I got it working. It looks like a problem of cart before the horse. This was a migration from 6x to 7 using the configuration backup tool. After the migration it was a week or so before adding Owncloud back in.
I had tried disabling owncloud for the users then reenable it but that didn’t work. What finally worked was to add in a new user with Owncloud privileges, then disable the old existing users Owncloud privileges temporarily. After reenabling the older users Owncloud, the quotas showed up. I did still get quota limit file size error messages while resyncing but after the initial resyncing I haven’t seen any since.