The 6d is a new camera. Is your acr/lr up to date - or does LR/ACR even support it? I suspected it was something with the raw conversion being funky (hence asking you to try JPEGs). Why it is suddenly working, I do not know. Unless.... When you say it is working from LR, are you sending the JPEGs to PS from LR, or are the raw files that were originally not working being sent to PS? I suspect that you are sending the JPEGs...? Even if you are sending the raw files and it is magically working now, it appears that the raw support for your camera may not be fully implemented yet.
So, if you choose a DIFFERENT image set in LR and use your LR -> PS HDR workflow, does it work as expected?
If your camera is not supported fully, then the raw conversion process has the potential to be a problem.
If you have an older model camera that is fully supported in LR/ACR, try shooting a raw exposure sequence with it and see if the problems with your LR-> PS HDR workflow persist. I am guessing the problem will go away. I can upload a sequence of 5DII images for you to test if you want.
I do not follow the release candidate schedule for LR, so take a minute to check in the Adobe or LR forums to see when the 6D will be fully supported, if it is not.
The current version of PSCS6 for Mac is 13.0.4, and ACR is 220.127.116.11. Bridge is 18.104.22.168. I am on a MacBook Pro, with OS X 10.7.5.
You are on the bleeding edge, expect turbulence!