I'm on Windows 10, using the desktop app. I have every option for notifications turned off, yet I still get desktop pop up notifications for 1on1 messages. The Flowdock Help page on notifications says I should be able to turn these off:
"You can adjust what you want to be notified for on the desktop from your Notifications preferences:
- All messages, including team inbox messages.
- All chat messages.
- Only 1-to-1 and messages with mentions.
- No messages."
I have also used Flowdock on Mac High Sierra and have experienced the same issue.