That is exactly what I have been doing. the images returning to LR with NO changes made at all in Photoshop are the problem
What version of LR are you using? 4.3 offers support for the 6D. Are you using the official 4.3 or a release candidate? Have you updated your PSCS6 yet (from 13.0.2 to 13.0.4) and your ACR to 7.3? Previously you noted that you were using 13.0.2 CS6, which is out of date - I assume you have not updated ACR to support the 6D either.
Until all of your applications in this tool chain are updated to the latest versions, it is not possible to help any further - the newness of the 6D is, in my estimation, the root of the problem.
Have you tried performing the operation with an older, fully supported camera as I asked previously?