App-V 5 Deployment Type fails to import in ConfigMgr

After creating a package of Adobe Captivate 8, validating that it runs as expected in a standalone scenario an obstacle come up during the import-process into the App-V 5 Deployment Type into System Center Configuration Manager 2012 R2.

Error code was very generic and only gave a vague reference:

Object reference not set to an instance of an object

Reviewing the activity with Process Monitor only revealed that the before the error occurred the appv-file was parsed. Obviously something within the file itself was generating this error.

No other application spawned the same behaviour, and regardless of how the application was sequenced (different OS, sequencer PVAD etc) the same error always came back.

Based on Microsoft supports reply it seemed to boil down to the fact that a package contained two files with the same name: AppXManifest.xml

The installer for Adobe Captivate generated this file in the following folder;
ProgramfilesCommonX64\Adobe\Adobe Captivate 8 app Packager\assets\AppxManifest.xml

The second file is the generic AppXManifest.xml generated by the sequencer that contains information of howto publish the application.

Workaround: Delete the second instance (not App-V 5 sequencer generated) copy of the file.