Hi 
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The logo is pinned separately and is probably been set to appear on all pages, where as the menu(s) are not.
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If you want them to be vertically aligned together, you can place them all inside a regular box and pin the box instead.
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Regarding the multi-state boxes they’re working just fine now.
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Some elements extend their height or width when changing the label or the text, for example, a word in English might take 20px wide, while in French in might take 35px wide, and if the element width is set to less than 35px, the text element will extend its height making a second row of text, causing it to “look” differently, so it’s a design issue not a code related issue.
Ahmad