Tuc,
I can honestly say that the reason for the inability to certificate the MR4 was not made clear to many of those in industry close to the process. I suspect that the fledgling MAA may have been involved in part.
A letter detailing around 10 failures to comply with DS 00-970 came from the PTL. The response to all of them was pretty much "true, and the PT was told at the time and given the reason why they were thought to be acceptable." While the letter came from the PTL, it seems likely that the MAA was the real source. Remember the MAA was relatively new to the certification process.
FWIW Leon J has already mentioned the only two real issues I recall.
EAP