"usr" doesn't appear in config.log at all. I can't find anything related to /usr/local/include in neither configure nor configure.in. ac_default_prefix is however /usr/local in configure.
Perhaps something gets confused by the fact that / is mounted as /usr.
$ mount C:\DOCUME~1\Nilsson\LOCALS~1\Temp on /tmp type user (binmode,noumount) C:\Program Files\MinGW\bin on /usr/bin type user (binmode,cygexec,noumount) C:\Program Files\MinGW\bin on /bin type user (binmode,cygexec,noumount) C:\Program Files\MinGW on / type user (binmode,noumount) C:\Program Files\MinGW on /usr type user (binmode,noumount) a: on /a type user (binmode,noumount) c: on /c type user (binmode,noumount) d: on /d type user (binmode,noumount) e: on /e type user (binmode,noumount) f: on /f type user (binmode,noumount) g: on /g type user (binmode,noumount) h: on /h type user (binmode,noumount) i: on /i type user (binmode,noumount)