I have those too, but only visible on completely white screen, so, I use a dark theme. Solved. You, know, so-I-won't-get-an-ulcer sort of fix. Just like I fixed the proximity issue by apologizing to people I hang up on, as well as as people I bother during calls because N900 doesn't tell me I'm waiting. All I have to do is call them and explain I'm an idiot and I accidentally randomly hang up on people.

See? All fixed. Where's my medication?

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ETA: The reason spots don't appear at boot time is because the phone is at higher brightness. AT 5/5, all my spots are gone. At 2/5, they reappear. Barely visible at 3.

Restoring backup restores settings.