I use firefox with stylish and a popular global stylesheet called "Carbon nitro - dark global style" link to the style. Problem is it blanks out certain images including the notifications box at the top left of stack overflow. I'm not sure if anyone would consider this a notable issue but it blocks users of text browsers from a significant piece of functionality. Thanks.
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The StackExchange™ MultiCollider SuperDropdown™ link has the text "Stack Exchange" in it, it's just shifted out of the way as to not obscure the background image using a pretty common CSS technique.
The fact that the userstyle you're using removes the background image but doesn't account for cases where the image was a replacement for text (by resetting the styles used to shift it) is a fault of that userstyle, not of Stack Exchange.