I remember trying that out on my buff / song windows way back when I originally coded them a couple years ago (just been too lazy to publish until recently) and it did the same thing. I havent really tried it in any other windows though, just wanted to point out that this isn't a 'new' issue related to the last patch, but a longterm one.
It's a shame though because it'd be really nice to be able to turn the border off those windows with the toggle.