First off, this situation doesn't sound any different from previous years, AMCAS problems or not. Keep in mind that MANY schools (even the "top" ones like Columbia or Wash U) may end up taking anywhere from 40-50% of their class off of the waitlist. This has happened in previous years -- there is no reason why it wouldn't happen this year.
As to why so many of you seem to be getting the waitlist notice rather than acceptances, one reason may be because LAST YEAR, many schools were having significantly slower waitlist movement and some schools were oversubscribed by 20 or more students initially. This resulted in a lot of lists not really moving until mid-June.I'm not sure why waitlist movement was so slow last year, but it was an unusual phenomenon commented on by several admissions directors. Anyways, some schools may be worried about possibly overfilling again this year, so they may be initially waitlisting a greater number of applicants.
Finally, interview comments really don't mean that much. I really hit it off with one of my interviewers last year -- he did the whole "You'd be excellent here... you should come to my clinic when you attend, blah, blah, blah." And then I got waitlisted (although ultimately got accepted). Keep this in mind when residency interviews roll around as well (there's actually a thread about this in the Residency forum) -- unless you actually get something in writing, these verbal compliments after the interview really don't mean anything and are no sort of guarantee of admission. Maybe your interviewer thinks you are awesome when you interview in November or December, but he still will be interviewing applicants for 2-4 more months -- things change.
In all honesty, going off of the experience of friends and SDN'ers, it seems like if you are on at least 3 or more waitlists, you have a very, very good shot of being accepted by the summer. Obviously there's no hard and fast guarantee about these things, and it is extremely frustrating, but more often than not, it seems to work out. Good luck.
Even at the schools (forget the backups) I felt like I had super awesome interviews, I was put on their waitlist. I still have yet to hear from one other school post-interview, and have one more interview to go, but I hate to not know if I will be in med school at all in the fall. 
