I have the same issue with the alerts but i'm fine with minimizing the apps to check email manually for now. I now have a problem with the mobile mail closing out instead of staying suspended/minimized.
I've already modified the phone settings to hide only so I can access my apps much faster but the mobile mail seems to stay minimized for maximum of 5 minutes. If I check after that, the app is closed and Im having to reload the application
Anyone else having this problem or have any idea how to keep this app minimized for extended periods of time. (I'm thinking maybe its the Yahoo email account that its interfaced with that keep logging out after no activity... hmm)
I had and have the same exact problems. I gave up on alerts ,don't use mobile email 2.0 anymore because It was too frustrating.
My solution - I use opera 5 beta 2 (be sure to get full screen and use TKFE) and open email through it. Opera has multiple tabs option so you can always leave email open while you surf, just hit refresh and there you go. I've minimized opera for days and left it going w/ no problems.
Very rarely and mostly when I've got several things open a minimized app might close.
Was messing with mobile email 2.0 just to torture myself signed out and got an email alert (no audio) through phone widget

had to sign in to read it

Hope this option of using opera will help you