I feel your pain. I had my application and all my documents sent in by mid November. By the end of January, a lot of my friends were receiving their acceptance letters so I decided to call Stony Brook to see what's up. I called on the 3rd and was told that they didn't receive my transcript. So naturally I freaked out and had my counselor fax and mail my transcript the next day. What confuses me is why I never received a notice telling me that they were missing my transcript those past months. I did receive an email yesterday about my missing transcript but I'm not too worried because I know it takes a few weeks for things to be processed.
If I were you, I would get my transcript in as soon as possible. Also, the representative on the phone assured me that this isn't a problem because they still have a lot of applications to go through. I can't help but be worried anyway because I still have to wait a while for any sort of decision and Stony Brook is my first choice. lol =/ Just get your transcript in and things should be ok. =)