I have just run into this same problem in 2014. I couldn't find a solution in the forums.
If I open the part files that are exported to the new P&G location, they are linked to the correct (copied) excel parameter spreadsheet. The assembly file that gets created from the P&G export is still referencing the OLD geometry, and consequently the OLD parameters. Now I have to replace ALL the components, which is not much fun.
Am I doing something wrong? Open assembly --> pack and go {copy to single path, include linked files, skip: libs, styles, templates}
Thanks in advance,
A
Update: I've started rebuilding my assembly and noticed that the P&G'd parts will no longer update with the paramater spreadsheet. The linked file is correctly listed but will not update as parameter values are changed; this is with both manual and automatic update options (from the Fx list).