I have this problem too. The issue is that if I check the apple store it indicates that there are no updates available, only the upgrade to the OS X Yosemite.
My OS version is OS X Mountain Lion (10.9.5)
I have the xcode version 5 (cannot check the exact version as it does not start).
Another thing I notice is that there are also 4 incompatible update highlighted (but there is no indication of what this means exactly or how to fix it. Anyway the 4 incompatible updates are on 4 applications which are not, I believe, related to xcode: iMovie, Keynote, Numbers and Pages).
Any advice?
Thanks