Based on the .BRD files, the connectors are in exactly the same spot on Duemilanove and Uno (using the "info" command on the connector part origins.) 5 mils is pretty tiny; it would be easy to be to get a Marker in the wrong place with most reasonable grids... I believe the "correct" separation is 160 mils.
The Mega and Uno-Mega connectors are apparently 10mils off (150mil separation), and have been all along. But no one noticed till people started going over the Uno looking for mistakes (most shields fit "ok") 5mils is about the minimum copper trace width for most PCB shops, BTW...
(and it looks like my Freeduinos are something like 168mil. I could swear I checked it a lot more carefully than that! Sigh.)