Where are you seeing the full name inconsistencies specifically?
In particular, the sidebar area when viewing a document. The section "More by..." shows the username rather than fullname. Also in the comments area, and other areas.
We have the exact same problem. We're currently running 1.3.
They are definitely using different properties. For example, full names show up using:
The users that show up with just username are are using something like:
Hope this helps,
I have now seen and verified the inconsistencies. They are just a result of not checking the system property before displaying the name.
I have recorded this as a bug here: http://www.jivesoftware.com/issues/browse/CS-1532