The conflict became about name after the aggressive irredentist rhetoric coming from newly-formed Makedonia in the 1990s. Remember that Greece had a civil war and Yugoslavia supported the communists in Northern Greece, so the subject is tricky.
I wonder - is this spelling some sort of shibboleth for Greeks who want to make a point that 'Macedonia' is only the area in Greece? I've seen it a few times in this thread, but never before anywhere else (then again, I didn't even know this was an issue until a week ago).