Tool windows that have a fixed size are too short. I think some of these windows are resized by the program while they are being put on the screen.
e.g. a window from OnTime:


This is very annoying, because I cannot choose anything within the window! Therefor I have to disable WB for this app. However, I have 3 apps that react like this, so using WB for all others while these apps look like normal Windows is a bit strange.