I experience this with a surface 3 Pro with Windows 10 tablet and a Windows 7 desktop computer. Exactly the same behavior.
The files are either local or on an external drive through a dock.
It works fine on a Macbook pro with OSX 10.10
all the three AME releases are 2015.0.2 but I experienced it with all earlier versions of AME
The only workaround I found is to use Premiere Pro to finish muxing the AAC and M4V files. But it's really annoying the have a batch of encoding suddenly stop (and sometimes restart) for no reason.