I was told that a few years back, when they first started to go electronic, AMCAS screwed up big time. Applicants were not able to access information, data was lost, etc... etc... In response schools ditched AMCAS and set up their own systems. Many later returns to the AMCAS system once the bugs were fixed, but some never did (NYU, Columbia, and so on...) This is, at least, what my premed advisor had told me.