SpamSieve problems after upgrade to Mavericks

SpamSieve 2.9.13, Mac OS X 10.9.2, Mail 7.2 (1874) – Picking up from AOL accounts after disabling AOL junk filtering:
When I installed Mavericks, Mail added a Junk folder and started putting things in it from my aol accounts. I read the suggestions on this website for disabling the server junk filtering. Since doing that, the junk mail from the aol accounts shows up in my Inbox, coloured to indicate they have been filtered through SpamSieve for spam-status. Training these spams as spam using the Message menu for that gets them moved to the Spam mailbox, but does not cause them to be put there next time they come through from the same sources.
What is the quickest way to solve this problem?

The mailbox was always there. Mavericks just displays it differently. Please see the Why does the “Junk” mailbox appear in Apple Mail? page.

There may be something wrong with your Apple Mail rules setup. Please see Checking the Apple Mail Setup and try the test at the bottom of the page. Or Mail’s database may be damaged; you could try rebuilding it.

seems OK now

I deleted the rule and put it in again. I couldn’t check it then because I had deleted all the spam. This morning once I trained two stray spams that showed up, everything has been working just fine. Thanks.

Problem came back
The problem came back the next day. I rebuilt the mailboxes both ways you suggest, but it has not changed. I have been observing it for a while, hoping I could say something helpful about it. This is a MBP which goes to sleep when I close the case. This problem never happens when the computer is on and awake. It only happens when I wake it from sleep. (I don’t usually shut it down and go away; the only time it gets shut down is when it is restarted for some reason, so I can’t say if it would happen after having been turned off for hours.) It happens when it has been asleep, I lift the cover and immediately there are emails in the box and more arriving – with spam just as I described at the beginning of this thread – coloured as though they had been through SpamSieve, and showing a brown Junk label, ‘you have marked this message Junk’. So I ask them to be trained as spam from the Message menu, they get moved, and then I go on with reading my real email. What do you suggest I try next? (It is almost as though iCloud/Mavericks had jumped to shove it into the Inbox before SpamSieve had had a chance to complete the sorting – awkward description, best I can do with it.)

Please see Using a Spam Mailbox on the Server. Sometimes that helps. However, there does seem to be a bug in Apple Mail (on Mavericks) that can prevent its rules (not just SpamSieve’s) from reliably moving messages after waking from sleep.

Since the messages were colored as spam, SpamSieve already classified them as spam, so you should not train them as spam.

what should I do instead?

What should I do instead? Anything? Delete them?

Yes, you can just delete them.