If font sizes are indeed different on Pd-extended, then that's a bug. From all my tests, they are pixel-accurate on all three platforms since 0.39.3. You might have the problem where Tcl/Tk can't load the fonts properly on GNU/Linux, which is addressed in this FAQ:
http://puredata.info/docs/faq/on-gnu-linux-the-fonts-are-strange-and- or-too-big-or-small
Otherwise, if you are indeed seeing different font/pixel sizes with Pd-extended 0.40.3 then please file a bug report with as much detail as possible and an example patch.
.hc
hans, I think matt was referring to font differences _on vanilla_ bet. different platforms. and font differences bet pdx and vanilla. but english is not my first language, maybe I am wrong... marius.
That's right -- differences between vanilla on different platforms, and between vanilla and extended. The point is, it's hard to ensure things will line up with nice, clean, right angles in all cases.
M