Why? 

I think we have been using SW for more then 20 years now (time flies). For years we exchange models with pack and go with co-workers outside our network so they can work on it. These pack and go compressed files copied the directory structure . When the co workers returned the files with pack and go / or zipped we could copy all the files into our system without any trouble.

NOW All part files are flattened to a 2 layer directory structure and all assemblies pushed into the main directory. With a big model we need more time to put assemblies and parts on the right place then to do the modification ourselves.

Any suggestion how to solve this or will this be rectified in SP1. 

We asked our reseller? They would file it as a whatever. Useless