I have two issues and not sure if Mail problem or SpamSeive or both.
It seems that Mail will bog down and fail to retrieve new mail perhaps most notably after a sleep/wake cycle or after several hours. Sometimes restarting the machine is needed to get things cleared up.
The drone moves junk mail to my server junk folder, but satellite machines are marking the mail as junk mail and leaving it in the inbox, perhaps as a ghost mail. Sometimes the mail will move on its own in a bit, sometimes I have to exit Mail and restart it for the marked mail to clear.
I thought these issues my be related to my 2008 Mac Pro being a little tired after these upgrades, but these same problems exist on a new iMac which is now the drone machine and of course on a fresh install of El Capitan.
I have tried some if the uncheck/recheck workarounds that I’ve seen in my research of any Mail issues with El Capitan. My Apple junk mail filtering is turned off in Mail, although the satellite machines appear to mark the mail as junk in “Apple style”, not SpamSeive coloring.
I also have SpamSeive set to not close with mail.
Any thoughts welcomed.