I think I may have figured it out after 2 days and posting this. Phew.
may i know how did you do it? i've the same problem too
I'm sorry forgot to post it!
Go into Mail > Preferences > General > New message notifications > Change it to "Inbox only."
Thanks, mine is already set to "Inbox only". However, I've solved my problem too. My Gmail account had both "Inbox" and "All mail" to show in IMAP. Disabling "All mail" under system label was the solution for me.