It also just might be the case that either the department or graduate school refuse to recognise the unofficial copy of your transcript as valid (for whatever reason), and want to work directly from the official copy.
I've had one school require an official transcript from one of my past institutions since they didn't like the look of the PDF-generated version (whatever that means). They had no issue with my other unofficial transcript though. All of my unofficial transcripts were from local, well-known universities, so they would have encountered them in the past.
That being said, hopefully it is just the admission process is a little out-of-sync and you have an acceptance en route; good luck!