Um, well, unfortunately a screenshot of "how it looks after it happend" doesn't tell me anything about "how it actually got into that state".
Are there any observable patterns? With regards to actual messages, their number, senders, anything?
Are you using "unified" Smart Folder notifications (app settings -> Smart Folder -> "Use for notifications") or the default per-account notifications?
What about app settings -> message notifications -> notify about -> "new" or "all unread"?