The problem is caused by how Tk and X11 measures window frames:
it measures it including all of the chrome around the window
(the button/title bar on the top, any framing on the bottom,
etc.) The window framing/chrome varies a lot depending on which
window manager, etc. you are using.
http://wiki.tcl.tk/11502
Pd-extended places windows based on how things measure using a
standard GNOME install, since GNOME is the default on most
distros.
So what you need to do is write a plugin that sets custom values
for your window manager. I think these are the variables you
need, but look in pd/tcl/pdtk_canvas.tcl for more info:
set ::windowframex 5 (play with the numbers to get it right)
set ::windowframey 5
Once you get it working, post it to the puredata.info/downloads
page so others can download it if they're using the same window
manager. There are lots of other things you can customize too,
so you could make a plugin that makes Pd feel as native as
possible.
.hc