I have tried to reproduce this bug and cannot, on mingw while building on windows and on mingw cross compiled on linux. The fact that your version numbers are screwy suggests something is wrong with your git repository and this may have nothing to do with cgminer. The correct way to build from git is to ./autogen.sh first, and not to manually use autoreconf (yes I know the docs are outdated). Testing a tarball release version instead of build from git should tell us whether that's the case.
This is funniest part, I get 2.9.0 from git and after compilation version tells 2.8.5...
Something break after 2.8.7-1.
Bad that git now tells me "-master" not "version-commit" like it was earlier. I have deleted earlier downloaded sources.