And you are using a 2.5x autoconf, which is needed for sane config.logs? In that case, and if /usr doesn't appear at all, then it would mean that the prefix scan is completely bypassed, which should only happen if both LDFLAGS and CPPFLAGS have been set manually. It's the section of configure.in which begins with
if test $ldflags_is_set = yes -a $cppflags_is_set = yes ; then :; else for dd in \ [...]
You might want to run "sh -x configure" to find out exactly what happens here.