Can you try running appcert.exe through a command line and check which step it fails? That way you can isolate it to a specific step in the certification process.
http://msdn.microsoft.com/en-us/library/windows/apps/hh694081.aspx
Open an elevated command prompt and then type the below commands. Appcert.exe will be present in: C:\Program Files\Windows Kits\8.0\App Certification Kit.
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appcert.exe resetappcert.exe test -apptype windowstoreapp -packagefullname [package full name] -reportoutputpath [report file name]
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