I don't know if this will help or not bgt28, but I also did not send any official transcripts. I did, however, scan an official copy and attach that. I don't know if the unofficial official is any different than an unofficial honestly. I've heard once you "crack the seal" on the official envelope it is no longer regarded as such. However this was for the literature program, NOT MTL.
Were you told by someone at Stanford about the transcripts?
I'll keep my fingers crossed that it works out in your favor though!