Hey Abe - I also have a google apps address and don't know how many times I've caught myself using mail.myapp.com or pop.myapp.com instead of pop.gmail.com. You might also want to try pop.googlemail.com port 995.
Double check that you're logging in with the full email address as well - xyz@myapp.com
Thanks for the tips, but unfortunately doesn't seem to be working still. I can send e-mail just fine from that account, but can't seem to receive any. I don't know what that is. I checked my setting numerous times, pop.gmail.com, pop.googlemail.com, even did that :995 or :587, but still no dice. I also made sure that it has my full email address. I kept looking at my mail.app settings on my laptop to do the same on the iphone, but even then it doesn't work.
We'll probably just have to wait for a fix, or until someone posts how they did it.
Abe