I am currently in the process of transferring my domains from Mydomain.com (which is part of Dotster) to Total Registrations (a UK-based registrar).
I am having exactly the same problem as the OP. Days or even weeks after they have been transferred away my domains are still showing in my Mydomain.com account, and Mydomain is still sending expiry warnings and expiry notices to the admin contact address. I've complained time and time again, but they don't seem to be willing/able to fix this bug. All that has ever happened in response to complaints is that they manually removed domains from my account with them.
Most of the domains are my own, but there are some customer domains, and just like the OP I have had angry emails/phone calls from customers who had been wrongly informed by Mydomain.com that their domains had just expired... when the truth is that they were happily sitting in my account with Totalreg with an expiry date a full year away.