Rob,
It says "xmkmf: command not found", which certainly explains the problem. It is a bit surprising that xmkmf is not there, but I don't know whether that's a a general problem with X on Snow Leopard or not. I did have to reinstall X at least once because the first time it (apparently) silently failed to install everything. Unfortunately, I don't have the media to hand to try again today. I think it is entirely reasonable to view this as a problem with the platform and not a problem with Poly/ML.
It seems that xmkmf has been dropped from Snow Leopard. See http://wiki.finkproject.org/index.php/Fink:xmkmf . This mentions autoconf as one of the problem areas and says: The "autoconf" ones are probably easy to fix (autoconf-2.62 has a fallback detection...
I built the configure script on Debian stable (lenny) which uses autoconf-2.61 . I'll try updating one of my machines to "testing" (squeeze) which includes autoconf 2.64 and see if that produces a configure script that works.
Regards, David