For some reason, the CSS for thickbox adds "* { padding: 0; margin: 0; }" to our CSS. This removes margins and paddings in a bunch of places. reosarevok noticed a change to the tabs in the release editor and all the checkboxes are now much smaller for me.
I've removed this in 60455ce5. However, as I can't actually test this it might have broken the ThickBox display. Once we have development environments I'll actually be able to test this a bit better.