That's not right. Send AACOMAS a transcript from each institution you have attended. They will receive them, update it on their website, perform the data verification, compose your e-profile, and then mail your application out to whatever schools you designated.
At this point, it may take anywhere between 2-4 weeks to process your application, depending on how busy they are. You should call AACOMAS immediately and see what the reason for the delay is. They were missing one of my transcripts at one point as well, but it turned out that they were backlogged in processing their mail (ie. they received it, but hadn't looked at it yet, and the representative did not know that until he actually checked). Chances are that your transcripts have not been lost, but do not make the mistake of letting it go. Call them ASAP.
Also, yes, you have a chance of getting in still for the class of 2009. I don't know how many people generally tend to apply this late into the cycle, but chances are, if you are selected for an interview around this point (from what I hear, some schools interview up till April), then you have a pretty decent shot of getting admitted. I'm sure they wouldn't waste their time looking at someone they wouldn't consider worthy of admissions, especially if they have to be more selective near the end about exactly whom they want to interview for the remaining number of seats. Bottom line is, you have a chance only up until the deadline. So, get on the ball, start looking at secondary essay questions that are posted on SDN, and write 'em up - once you're processed, you can get 'em all out very quickly.
Once you're admitted, and you decide to matriculate at XYZ School of Medicine, then you will be required to forward each of your transcripts to them. Do not do this right now. Send all your transcripts to AACOMAS; make sure they have them.
