Ok, I might now be able to shed at least some light on this.
Firstly, looking at the LR5 DNG vs. the LR6 DNG:
1. They are the same in that they BOTH have the "20130317 Jeff and Pauline Venning 3" profile set in IFD 0. Why exactly this is occurring I'm not sure, but this behavior seems to be the same for both LR5 and LR6, and doesn't contribute to the issue.
2. The DNGs differ in two ways:
a) The LR5 DNG has the "5D Mk2 Dual Illuminant Profile" embedded as a second profile. This is not present in the LR6 profile.
b) The LR5 DNG also has adjustment data (exposure adjustments, etc) embedded into its XMP data. Critically, this data includes the following line
crs:CameraProfile="5D Mk2 Dual Illuminant Profile"
So what appears to be happening here is that when LR6 imports and converts to DNG with a profile, it does not create an XMP adjustment record. So when the DNG is written, both the profile and the profile assignment are missing.
However, if you adjust the image, and then write it out, and XMP adjustment record is created, and everything works as it should. I think that this is why the second test worked - "I then made some adjustments" being the giveaway.
In summary, I think that under LR6, import and assign profile is not enough to mark an image as "modified". If it's not marked as modified, then adjustment data isn't written, and you get the problem as described above.
It would be interesting to try to import with a preset that both assigned a profile and made e.g., a small exposure adjustment, and see if the problem persists.
I'd agree, BTW, that this is a bug.
Sandy