This is a problem that I have always had with my first and even my second storm, on all OSs.
Whenever I open the applications folder, the menu will jump down and row or two, but now with 5.0, it scrolls down four rows upon clicking, and it's really annoying.
Why does it do this? This used to happen about 50% of the time, but now with 5.0 it's almost every single time.
This happens in my Downloads folder. I don't have enough icons in my Applications folder to test it. I guess the only answer to your question is that it's a feature, not a bug.