You're not alone. I have posted on two or three other threads regarding two email issues plaguing the iPhone since Version 2 was introduced.
I have a 1st generation iPhone that worked impressively and flawlessly for months before I blundered into Software version 2.
I'd gladly abandon the two web apps that I installed if I could wave a magic wand and go back before that fateful day that I made the mistake of updating.
For the record, I have 5 POP accounts, all from the same ISP set up.
Since Version 2, I first encountered the situation where several times a day, the iphone would try to fetch every fifteen minutes as it did like clockwork since the day I brought it home, but would get stuck trying to get the mail. The only way to get it unstuck and to get the mail was to shut the phone down and restart it.
This last update "fixed" it so that even though it is set to fetch every fifteen minutes, it only very rarely fetches while unplugged in standby mode, until either the phone is wakened or until I open the email application and peer inside.
I use my phone for business and I have become so desperate for a fix that I have resorted to checking for an update every day.
This is not the Apple Computer to which I was once loyal.