This article discusses a specific crash that can occur while building the repackaged application
While trying to build your output from with in the Repackager it will get to the point of building the context.msi package, and the islc.exe will crash.
This can happen if the .NET 3.5 feature is not enabled on the operating system the Repackager is being run on.
If you are seeing this behavior during the build of your repackaged application you will want to enable the Windows Feature for .NET 3.5. The easiest way to do this is to hit the Windows key, and start typing "Windows Features". This will bring up the "Turn Windows features on and off". From in where select the .NET Framework 3.5.x feature. Once this is installed you can try building the project again.