It's been getting worse and worse for me. It doesn't actually filter incoming mail until I click in and out of the inbox once or twice. I have to visit every inbox (one per account) and then let it churn to check for spam, then it still doesn't move messages to the Junk folder until I click in an out of *that* folder. Once I do, it finally starts downloading for offline use, and if I delete anything before it's done downloading it throws errors. And it hasn't highlighted (per rules) for a while now.
There are so many annoyances I think there's got to be something wrong with my installation, but I've deleted and reinstalled several times. I tried going to the latest dev branch, reverted to stable, etc. I'm running out of ideas.
I know there are other options, like Thunderbird, but I really like the Evolution UI ... when it's working.