For others who this might affect, I discovered that the new beta version of MailTags 2 introduces a keyboard shortcut conflict with SpamSieve, and (I assume because M comes before S alphabetically) coopts Command-Ctrl-S for its save to IMAP function (taking away the keyboard shortcut for Train as Spam).
I’m not sure if this will be changed in the release version of MailTags 2, but (as briefly touched on in the SpamSieve documentation), this can be worked around. Going to the Keyboard & Mouse system preference, and adding a new keyboard shortcut for Mail, menu entry “Save tags to IMAP”, assigned to Command-Ctrl-I (or whatever one wants for the MailTags command), removes the conflict and restores Command-Ctrl-S to Train as Spam.
Given that both MailTags and SpamSieve are popular Mail plugins, I imagine that the conflict will arise for other people, so it seemed worth posting the workaround.