Did you clone the actual multi-image drive and create the R6 image on the BDM50 system in question or did you use a cloned image that was created on another BCM50 R6.
I have created virgin images of all BCM50 revisions from the multi-image drive. It then only takes a few minutes to create a new drive from the correct cloned revision instead of building a drive on the BCM50 that needs a new drive.
I have found that using a drive with an R6 image that was created on an original R6 works fine on an original R6 system but if you put that same drive in a system that was upgraded it displays the same symptoms that you are describing. I believe it's systems that were upgraded from R1 or R2 to R6 that have this problem.
I noticed this one time when I wanted to make a new drive for a R2 system that was upgraded to R6. On boot up of the multi-image drive it would only give me the choice of creating a drive for R1 or R2 even though the system was upgraded to R6. I imagine I would have had to create an R2 drive and then upgrade it to R6 to accomplish to create the drive. Instead I had another working system that was an R2 to R6 upgrade. I then cloned that drive and put it in the sick system, reset the programming, added the license file, reprogrammed and away she went.
It was a few years ago that I did this but at the time I did a little investigating and found that the boot partitions on an original R6 drive and an R6 that was upgraded had different names for the boot file. I suppose the boot loader on the upgraded system is trying to load the wrong file, can't find it and then craps out.
