Im getting the RAW error and general ETTR inconsistent performance when used with the intervalometer too. Problem hasnt rectified itself after i switched to ML nightlies either (6D).
In my experience raw is still buggy on the 6d, no matter TL or ML, the problem is that the raw dev (alex) doesn't have a 6d camera to test.
It helps if you at least turn off jpeg and *only* shoot raw, this at least is a known issue. For everything else, try to isolate the exact circumstances and make it reproducible, then post a bug ticket instead of cross-posting in the forum.