I just purchased this app today and it seems to work well with my GMail accounts but is causing a major issue with my POP accounts.
I am in Canada and use Rogers as my ISP. Whenever I add one of my Rogers accounts, my iPhone can no longer retrieve any e-mail from that account, and neither can my Mac. It is like your server is pounding my Rogers account and it cannot respond to my login attempts. As soon as I remove the Rogers account from Mail Notifier I can access my e-mail.
Ok, so I was trying out another app, IM+ Lite, for chat and such. I noticed it supports push notifications for Yahoo! e-mail accounts, which Rogers actually is. For the heck of it I added my 3 Rogers/Yahoo accounts. What do you know but wham, every single e-mail that comes in gets a push notification. It doesn't cause any problem with my e-mail access from my desktop.
The iPhone is supposed to natively support push for Yahoo, but it never works. I don't know what the developers for this other app have done but it works.
So I don't know if you could add Yahoo! support, instead of full POP support to your app?
Thanks