The Mobile Publisher was updated a couple of years ago to increment build versions each time you created a new build of your app. This has stopped working but will be fixed for the next Mobile App release (1.11). If you're rebuilding an app on the same version number between now and then, it will build with the same version number as previously and fail to update within the App stores.
In the meantime, you will need to edit the info.plist file and change the CFBundleIdentifier value to increment the final digit (e.g. 1.10.1) manually before resigning.
In the meantime, you will need to edit the info.plist file and change the CFBundleIdentifier value to increment the final digit (e.g. 1.10.1) manually before resigning.