I found a solution to the GNOME/metacity blocking the raising of windows. It turns out to be not too bad. Basically, you just have to 'group' each window with the toplevel '.' (i.e. the Pd window), then you can raise windows. Here's the commit for Pd-extended:
http://pure-data.svn.sourceforge.net/viewvc/pure-data?view=rev&revision=...
I am going to try adding this on pd-devel now...
.hc
----------------------------------------------------------------------------
"It is convenient to imagine a power beyond us because that means we don't have to examine our own lives.", from "The Idols of Environmentalism", by Curtis White