Had to re-run the configure in the failed build dir manually.
rm config.cache ; CPPFLAGS=-I/usr/X11R6/include ./configure ; make
freeglut 2.2.0 here
To be compatilble with glut it also needs the same library version, currently 3.7 for the glut I have. The current glut version could be 3.8 as is the name of the freeglut library but the version information in the library is set to 12.0 which is incompatible.
Closing out bugs that've been resolved for a while now...