Came here in search of the same issue after my upgrade to Big Sur. My original setup (with the problem) was:
- 2 Account-based rules sending spam to server mailboxes. One SS rule caught my Exchange account spam and moved it to a mailbox on the exchange server. The other SS rule caught my multiple Gmail account spam and moved them to a single mailbox under one of the Gmail accounts.
After the upgrade to Big Sur, spam was staying in my Mail.app mailbox, but it took me a while to realize it because looking at my inbox through Spark or iOS Mail looked correct. Using the Gmail web interface also looked correct, so it’s simply a matter of Big Sur’s Mail.app doing something wrong.
I was able to keep my same setup, but using Michael’s hidden SpamSieve preference: x-spamsieve://default?k=AppleMailPlugInSetIsJunk&v=NO seems to have fixed the issue for me (for now).
I guess we’ll see what happens when 11.1 gets released next week