Yosemite Issue: suspect SpamSieve

This is the behavior:

A subset of emails are being sent to a subfolder within the Junk folder.
They are marked with Apple’s Junk color, though Apple’s Junk mail filtering is NOT enabled.
I cannot mark them as Not Junk within the contextual menu.
If I invoke SpamSieve’s “Mark As Good” keyboard shortcut (Command+Control+G) only then are they made good, moved to the inbox, though they retain the gold junk mail text color.

This behavior is not present on my Mavericks machine which is up to date for both Mail and SpamSieve.

SpamSieve does not mark messages using Apple’s Junk color, nor does it use the Junk mailbox. My guess is that the message are being moved by a server junk filter. Or, it’s possible that Mail is moving them because the server flagged them and you had “Trust junk mail headers in messages” checked in the preferences. Of course, there is no need to guess about what SpamSieve is doing, since you can see in its log which messages it processed.