After some investigation the problem was, in my situation, that if you had your AppleID setup for two factor authentication, Apple is now requiring an app specific password to be used with Xcode and Application Loader since this new iTunes Connect upgrade. Neither tool will take your regular AppleID password on the account under preferences anymore.

The information on how to add such passwords onto your AppleID account is at this Apple support link Setup application specific passwords for an AppleID

Once I used the app-specific password instead of my AppleID password, Xcode 7.1.1 and Application Loader 3.1 was happy and completed my archive validation and export and submission for TestFlight as usual.

Message from Monaca while trying to upload to Apple Store:

We attempted to submit your application to App Store Connect, but had failed due to the following reason:

Error publishing to App Store.

Please correct the issue described above and try again.

Bug has been fixed

Remove the file " local_properties.json " of project and “Remote Build” again.

I found a bug in LocalKit when trying to do the “Remote Build”.
Explanation: When I change the config.xml file of any project local and do “Remote Build”, Localkit is not uploading the config.xml file correctly.

Example: Change the <name> tag of config.xml local and click on “Remote Build”. The system displays the “App Settings / Application Name:” field with wrong content.

When I create a new local project and do the “Remote Build”, LocalKit ALSO is not uploading the file properly.

Remove the file " local_properties.json " of project and “Remote Build” again

Problem has been solved!!!

The problem was that the project had a “google-services.json” file that was in the “UTF8 With BOM” format. I turned this file to “UTF8 Without BOM” and Build worked!

When doing an Android Release Build on Monca LocalKit, the following error is occurring:

• postBuild -
  Remove working directories…
  Build Error: Error: Sandbox Exec Error: [ Error: invalid data
  ]