Two aspects in the same issue.

1. Fixed Window
When you call up the Quick Build List in Civ Manager, its centered on the screen with a fixed window. It can block out the entries underneath to a substantial extent, and you cant move it. I run the game on 1650 x 1050, and even at that res, it blocks out a fair number.

If the Quick Build Window was made 'Floating', it could be dragged to one side depending on what you need to do on the Civ Manager screen. The functionality of the creen is excellent in that you can keep it open whilst clicking on separate lines working on whatever you need. However many times the fixed nature of the screen means you often have to close it to get at the next object to work on. Opening and closing that screen on a list of 100+ planets is tedious at best.

Biggest effect is for the bigger games with 100+ planets on the Civ Manager. With me Murphys Law always seems to apply and it sits nicely over the part I want to work on   

2. Main Screen Default
The second aspect of the Build Screen, is the underlying behaviour of the main screen. When you are working on a long list of planets, the tendency is to start from the top and work down either on the whole list, or a sorted element of the list. When the improvement has been bought/changed in the build screen, and you are in the situation where you have to close the Build Screen before moving to the next target to work on, the underlying main screen defaults to the top of the list you were viewing, forcing a scroll down to get to your next target. That slows down horribly navigation when working on large planet lists. The main screen should stay on current view, not redraw to a default "top of list"

Combine the two effects above, and they can often negate what is excellent functionality in the Build Screen, and turn the use of it into a nightmare. Again, this mainly effects Large Maps and above due to the size of the planet list.

Regards
Zy