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We've just noticed this same problem with Python 3.1.2 on Mac OS X.
The problem is that the program source in the configure script has extraneous '[' and ']' characters in it, causing compilation to fail.
Excerpt of configure from line 17357:
 cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h. */
 [
 #include <sys/stat.h>
 #include <unistd.h>
 int main(int argc, char*argv[])
 {
 if(chflags(argv[0], 0) != 0)
 return 1;
 return 0;
 }
 ]
 _ACEOF
These extra '[' and ']' characters were added to configure.in in revision 74038:
http://svn.python.org/view/python/trunk/configure.in?r1=74033&r2=74038
I have locally modified my configure.in and configure scripts to back out that change, and found it resolves the issue.