Some Administration settings are lost during a Vault upgrade. From the most recent upgrade (2012-2013), I remember at least Working Folder and Project File settings were empty when starting the new version. There might be more.
Also, most or all of the User-specific client options get reset to defaults in both Vault Explorer and the CAD addins. The ones that are most tedious to restore include grid columns and shortcuts in VE, and prompt settings in CAD addins.
If we're going to have to do a product upgrade every year just to keep current, please make it less painful.