Reproduction steps:

1. Open any project and build with IL2CPP
2. Open the generated solution and try to generate a package (Solution -> Store -> Create App Packages)
3. Fails with following output:

2>MakePRI : warning 0xdef00520: Invalid qualifier: DLL-RESOURCES
2>MakePRI : warning 0xdef00520: Invalid qualifier: DLL-RESOURCES
2>C:\Program Files (x86)\MSBuild\Microsoft\VisualStudio\v14.0\AppxPackage\Microsoft.AppXPackage.Targets(1433,5): error APPX0002: Task 'ExpandPriContent' failed. Could not find file 'F:\Work\Metro\_BUILD\SetInput\build\obj\SetInput\Win32\Master\split.pri.xml'.
2>C:\Program Files (x86)\MSBuild\Microsoft\VisualStudio\v14.0\AppxPackage\Microsoft.AppXPackage.Targets(1433,5): error APPX0002:
========== Build: 1 succeeded, 1 failed, 0 up-to-date, 0 skipped ==========
========== Package: 0 succeeded, 1 failed ===========

Workaround: when generating AppX package, select "If needed" setting for "Generate AppX bundles", rather than "Always":

http://i.imgur.com/ZOcKWsg.png