Make sure your .p12certificate file was signed and generated properly. If not, then you would need to generate the certificate again. Download Publishing Companion Guide given at https://digitalpublishing.acrobat.com and look for Certificate Creation Procedure.
It could be a problem when any one of your certificates has been created using a different name or computer. It would not be possible to upload binary/distribution-viewer.zip (built from Viewer Builder) signed with a distribution certificate created on a different computer). Viewer Builder does not have any problem building the app, but you will get this error Application failed codesign verification.
When you create certificate request in the keychain tool. This creates the private key and is stored deep in your user profile on the machine.
In this case, "The Keychain account should be the same for all of your certificates. Also make sure that iCloud has not been enabled for the application."
Create new certificates on your computer, use new certificates in viewerbuilder, download distribution.zip and upload to itunes.