A few questions: Which OS version? Are you mainly using Chrome? Do you have window transparency on?

Very strange. I am using the same vintage of machine (and have been for a while) but I've never seen what you're describing on mine. Do you have any special settings, or is there anything in particular you're doing on this machine (like a lot of videos, or an unusual web browser, that sort of thing) ?

Did it ask you to "Move to Applications?" and how did you proceed with that?

I'm curious because in this mac area, a few people have had a few issues, and I want to save some work for the f.lux team with the simple stuff.

You're welcome, have a great day. ^_^