I downloaded Xcode 7.1 from the App Store today after working from 7.1 beta downloads from developer.apple.com and have a new iOS app build to upload. So I did:
Same problem here. Downloaded Xcode 7.1 from the App Store and it refuses to upload a new version. Happily Application Loader worked ;) Hopefully this gets fixed quickly.
One possible reason for the issue could be multiple development accounts under one name (personal and company). I've read elsewhere (apple radar) that that caused earlier problems of this kind.