There is some problem with hlslcc which we haven’t narrowed down that causes it to report incorrect number of samplers in the generated GLSL. Could you share the details about your distro - that would help us find a more reliable repro. We have seen it on Ubuntu 14.04 only and even there the repro was inconsistent.
Also, try putting this into DefaultEngine.ini:
[DevOptions.Shaders]
bAllowCompilingThroughWorkers=False
bAllowAsynchronousShaderCompiling=False
This will make startup times much longer, but may avoid the bug.