Why didn't you just choose to Hide the toolbar, rather than manually removing each item?

Undoubtedly, the system API for the toolbar is a bit confused at being visible, but with empty content, and this is messing with the window height.
Right click the toolbar area and select the 'Hide toolbar' item.
However, I would suggest that you restore the toolbar to its default state first, by selecting 'Customise toolbar', then drag the default set to the toolbar and click OK. Then hide the toolbar as above.
Currently there isn't a way to hide the back/forward etc buttons, but I'm working on a UI update...
