Starting with SolidWorks 2012 SP2 the process has changed for upgrading a previous major version SolidWorks Toolbox dataset to 2012 when Toolbox is being managed by SolidWorks Enterprise PDM. In addition to the Toolbox upgrade procedure being revised, SolidWorks 2012 SP2 also contains fixes to ensure vaulted Toolbox datasets are properly updated to the new 2012 folder structure.
If you are updating a previous major version Toolbox to 2012 and that Toolbox is managed by SolidWorks Enterprise PDM, then this update should be done using SolidWorks 2012 SP2 to avoid Toolbox folder structure and Toolbox file location problems.
Please see Knowledge Base Solution S-058099 for the revised SolidWorks 2012 Toolbox upgrade procedure when Toolbox is managed in a SolidWorks Enterprise PDM vault.