I have the same problem. Usually it is most problematic when trying to preform a search or enter data on a form and, once finished, the only way forward is to press a button on the screen that is hidden behind the keyboard. There's no way to press it until the keyboard is removed from view, and there's no way to remove the keyboard from view! Pressing the back button only take you to the previous page and you loose the data you have already spent valuable time carefully entering and must now enter all over again with no guarantee that you'll be able to advance once you have.
It a major shortcoming of the phone and or the Android os.