I tried using the green flag feature. The messages were flagged (GMail) but the green flags were not removed after I read the message. Also, all of I sudden other messages were getting red flags. Is there a known issue with flagging and certain email services?
Did you move the messages from where they were when SpamSieve flagged them? It only unflags messages that are in the inbox or in another mailbox that it’s configured to filter. This will happen as often as you have it set to check for new unread messages.
It’s extremely rare, but some mail servers do not seem to support Apple Mail’s colored flags feature, and so they will change all flag colors to red.
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Thank you, Michael! 
I will double check.