I keep being told that it's because these icons aren't using the new
GTKStatusIcon, but that seems like a cop out to me.

A few releases ago (possibly Intrepid) this problem appeared in every
tray icon. It seems to be true that some applications have fixed the
issue by using GTKStatusIcon, but I don't think that's the root cause at
all.

Something regressed in whatever the icons were using before, which
triggered this problem, months ago.

That's what it seems like to me. I'm open to be proven wrong, but I have
a pretty clear memory of all of being able to change my panel colour,
transparency and even add an image without the icon backgrounds being
broken.

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Notification area icon wrongly rendered/has a black background (multiple apps)
https://bugs.launchpad.net/bugs/403135
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