I am currently implementing a prototype of Lisa Tweedie's answer to my question about having too many checkboxesmy question about having too many checkboxes.
The prototype I am building will look quite similiar to this: 
Problem: I am working on a 24 inch monitor, so the screen looks like this:

download bmml source – Wireframes created with Balsamiq Mockups
I am designing to fit the lowest resolution of 1024 x 768. If I do so, the mockup becomes (double scrolling problem):

Should I just get rid of the scrolling div and use the window's scroll bar? Is there any benefit to using the scrolling div, if we ignore the issue of double scrolling? Even then, on a large monitor, if the content is long enough such that the window can scroll, the user can scroll the window to a point where the scrolling div's scrollbar will not be fully visible.
Besides being used in very small scrolling divs and light boxes like these, is there any use for scrolling divs on a page?:

