This weekend I was setting up my new PS3 Slim and needed to transfer the data I have from my old 80GB PS3 but ran into some connection trouble. The problem was a timeout error stating that the systems weren't connected via an ethernet cable when they were.
I followed the instruction manual but after researching online at least 2 key steps were missing. Make sure you disable the Internet Connection and Media Server Connection on both systems. You'll find both options in the (Settings) > (Network Settings) area. Once I did this the data transfer worked.
When you attempt to transfer again it might take several minutes to connect (was about 5-10 minutes for me) so be patient!