I cannot reproduce this, but hit a different bug instead.  ;)

The configure script does not *create* the Modules/ directory in time to write the Modules/Setup file on the first run, so there are failures later.  This is fixed in configure.in revision 1.176.

I'm leaving this bug open, but assigning to Jeremy for further testing.  Please make sure you're starting with a clear working directory, or document what's there when you run configure for the first time.