Two years ago, I had the same problem. No one had my junior high transcripts, and that was the fact. What the school was doing at that time, was having you sign something that said you were gonna go through fifth pathway. The junior high records were just required to get the MD from the UAG (which at the time, was only available by the six year route). What has happened since then though, is that now the only options available are the five or six year MD routes, by through the UAG. So, I'm sure they have to make provisions for anyone already in the program that is missing the document. But, the bottom line is that this is just one of many details that they haven't sorted out and made clear yet since the changes. From what I've seen since being here though, they seem to be able to change whatever they want to change.
Despite all my rage, I'm still just a rat in a cage.