When my phone is in portrait view and on the main screen with only two lines showing, the icons are not working correctly. When I get a message, the message icon never changes. It is constantly showing that I have a facebook message when I actually don't, and the weather icon doesn't update. When I switch from the portrait view to landscape, or hit the BB key to get to the entire list of applications everything is correct. I am running .90, and have the default theme with a custom background.
Trust me, the battery pull is the answer. It's weird, sometimes when these darn things reboot if they aren't in the right position during startup they can show odd things on the portrait screen. It took me 13 tries one night to get my Yahoo icon to show connected while in portrait. If I switched to landscape, or the full list it would show the nice connected happy face, but if I went back to the zen screen it would show a sleeping face as though I was disconnected. Other examples are it would say I had a VM, or an e-mail in zen, but not in full portrait or landscape. I just kept doing a pull until it stopped. What I found to help though is to make sure the phone is not moved during a reboot. I pull the battery and keep it in a portrait view and set it down until it is completely booted. It seldom happens now.