Fixed sized tool windows are too small

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.
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Here is the tool window without WB:


BTW: Using Vista Ultimate and the 'Adamant Transparent (Vista)' skin