I had problems when I moved /bin to /usr/bin -- /bin/sh was no longer found. So, I kept /bin. Other than that, I tried your directory structure. My directory structure is now: / /bin /etc /i386-cygwin32 /include /lib /include /local /bin (empty) /include (also empty) /lib (also empty) /lib /var (empty) My C-shell path is set thus: I did notice something interesting before the configure script ends -- config.status is empty despite the "cat > config.status << EOF" piece of code in configure. I'm not exactly sure why it's empty -- I tried "cat > config.status << EOF" by hand and it worked peachily when done interactively. My current theory is that my bash is somehow broken, perhaps because I'm using "tcsh" as my shell. But, I'm not exactly sure why. I'll try running "pure" bash and see if my problems go away.