jScrollPane and Drupal: Content overflow while scrolling (better solution?)

Question

I'm currently trying to use customized scroll bars in Drupal. This with jScrollPane which is relying, like Drupal, on jQuery. The problem is the following. Usually the page looks like that:

http://granjow.net/uploads/temp/drup-jscrollbar1.jpg

Now, during scrolling, some boxes flow over:

http://granjow.net/uploads/temp/drup-jscrollbar2.jpg

Why is that?
Is there perhaps a better solution for custom scroll bars?

I've previously tried http://livepipe.net/control/scrollbar but this was not a solution either because prototype destroyed jQuery (but the issue named above does not exist here; Don't know whether this is related to the fact that Drupal is using jQuery heavily in the displayed area though).