Could you try packaging a blank C++ project? The fact that you could build UHT (Unreal Header Tool) but not the project itself is baffling.
By the way, if you need to just package a project, doing this on Windows (using Linux cross-toolchain) is better - it will produce a binary that works against glibc 2.12. If you package on Linux natively, you will likely produce a binary that will only run on distributions that have glibc version no earlier than your own.
Try non-unity build of your project. You are probably including headers in the wrong order or omit some header.
Regardless of the success of the build, I strongly suggest do a final packaging on Windows due to abovementioned glibc compatibility. In the future we will provide similarly stable Linux toolchain that will be independent from the rest of system.
