The configure.in for Miller's 0.39-2 (and CVS) makes the assumption that Darwin is always big endian and defines -DPA_BIG_ENDIAN. I manually changed the resulting makefile to the little endian flag for Pd to work. Also, I used the version of Tcl/Tk that comes with OSX which is in /System/Library/Frameworks/ so I changed that in the makefile as well.
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"Computer science is no more related to the computer than astronomy is related to the telescope."
-Edsger Dykstra