That happened to me with my transcript AND my GRE scores. I sent my transcript via UPS but it snowed the next day so things got delayed, sent back, etc. So I sent another one out the next and it didn't get there till the day after the deadline. I sent them an e-mail explaining the situation (hoping they'll make an exception for a late transcript) and, although it took a while, the status online was updated.
For my GRE scores, I sent it a month before the deadline and for some reason the status online still said it wasn't received. I e-mailed them and a few days later (maybe about a week?) the status was updated to received.
They don't respond to e-mails. So if it's been a while since you e-mailed them, and your status hasn't yet to be updated, I would call right away before they write you off for not having sent your transcript.