Certain emails moved to junk (through Spamsieve) without spamsieve score

You can try searching the following file for any move-related actions (search for “rules” or perhaps “move”):

~/Library/Application Support/MailMate/Mailboxes.plist

Even more low-level, but possibly useful would be to define an extra message list column. For that, you need the following:

{
    columns = {
            oldmailbox =
            {
                    title = "Previous Source Mailbox";
                    sortKey = "#old-source.path.noinbox,#old-source.#name";
                    formatting = { formatString = "${#old-source.path.noinbox} – ${#old-source.#name}"; };
            };
    };
}

This needs to be saved in the following file (you need to create the path):

~/Library/Application Support/MailMate/Resources/MmMessagesOutlineView/outlineColumns.plist

Then relaunch MailMate and enable the “Previous Source Mailbox” column in the junk folder. If the message does not have a “Previous Source Mailbox” then the message was most likely moved by the server or another email client.

I hope this helps.

The Mailboxes.plist file does not contain anything related.

The file Resources/MmMessagesOutlineView/outlineColumns.plist does not exist, there is also no subdirectory Resources inside MailMate..shall I create the directory structure myself?

Yes, you need to create that path (I'm sorry I didn't emphasize that).