Okay, so this isn't entirely related but it doesn't seem worthy of a thread itself.
I haven't removed the battery so haven't noticed your problem, but has anyone else noticed that when you restart the phone it forgets some of your app choice defaults?
Example: I use Go SMS, but after a restart when I click on my messaging icon on the homescreen it asks me if I want to use Go or or the stock app. It also happens with using Opera instead of the stock browser.