I may be mistaken, but I thought this was a limitation with iTunes. The library sync-ing is one way only and is not shareable with another hard drive, which is in essence what the second instance of iTunes represents. I went through a similar situation a few years back when I upgraded from an eMac to an iMac. There was no copy over procedure for iTunes libraries. I don't know if this has changed any.
Regards,
Rich
Regards,
Rich