I had this problem 4 years ago, and I have searched everywhere but can't find how I fixed it.
The Build Model" command runs. It creates a board part. Even tells me the process is complete.
Creating new SolidWorks component.
Using existing board model.
But the assembly is completely empty, not even the board part. Nothing in the tree.
All of the required models are in the library.
Everything was working until: I upgraded to SW2014 to do some testing, but had to roll back to SW2012 until the rest of the company is ready to upgrade. I rolled all the way back to 2012 SR1, because of the library bug that showed up in SP5. And I can't find an SP4 download.