I would imagine a good thing to do when building a new version is definitely to run 'make distclean' first to clean out old configs as well, especially if the build process has changed. Even better would be to just 'sudo rm -r
I realise this was not the original posters problem in the end, but just though it should be mentioned for when people compile other things.
Alex
I have a build.sh file in my cgminer git working directory that I run every time I want to build cgminer. It looks like this:
make distclean
CFLAGS="-O2 -Wall -march=native" ./autogen.sh --enable-bflsc --enable-icarus --disable-opencl
make
mv -f cgminer cgminer-nogpu
The 'make distclean' may not be necessary every time, but it doesn't take long.