I’m still on Ventura, and I upgraded to SpamSieve 3.0 (Plug-in). I have noticed that rules I have set up to color my inbox emails are not being processed any more. I can run rules on my inbox manually, and they work, so I know my rules still work, but they just don’t run automatically.
For reference I have my SpamSieve Rules above my color email rules.
If you have Filter spam messages in other mailboxes selected, that will color messages by spamminess, and part of that is removing colors of messages that are not spam. The idea here was to clean up messages when they get refiltered if they are not actually spam, but I can see that this would be undesirable if you are purposely trying to color your good messages. I will think about changing this behavior or perhaps adding a setting.
That said, in your situation it seems like you could just uncheck Filter spam messages in other mailboxes. It’s normally not needed with the plug-in setup, because the plug-in will filter all incoming messages regardless of which mailbox they end up in.
If you are switching to the extension, you should remove the SpamSieve rule in your first screenshot. There’s currently no way to prevent the extension or Filter spam messages in other mailboxes from cleaning the background color, except that you can set up your rules so that certain messages bypass the extension (if they are moved to another mailbox that is not selected or filtering). I will look into addressing this in an update.