Windows is case-insensitive (more precisely, case-preserving). There is simply no possible way for two files to exist whose names only differ in case: two filenames which differ only in case are the same filename. Period.
So, Git is walking the repository, checking out one file after the other, until it hits the first one of the two problem files. Git checks it out, then goes further about its business until it hits the second file. Again, Git checks it out. Since from Windows’ point of view the filename is the same as the first one, the first file simply gets overwritten with the second one. Which now makes Git think that the first file was changed to have the same content as the second one.
Note that this has nothing to do with Git: exactly the same would happen if you had a tarball, a zipfile or a Subversion repository.
If you want to do development on multiple different platforms, you have to respect the restrictions of those platforms and you have to confine yourself to the lowest common denominator of all the platforms you support. Windows supports ADS, Linux doesn’t. OSX supports resource forks, Windows doesn’t. BSD supports case-sensitivity, Windows doesn’t. So, you can’t use any of those. That’s just the way it is.
core.ignorecase isn’t going to help you here, because that handles exactly the opposite problem.