I went through the recent issues and this got my attention:
I noticed that something has changed regarding renaming the Putty Tabs with the recent RoyalTS version. I tried disabling this functionality on a SSH Connection:
Properties - Advanced - Features - “Disable Remote-Controlled Window Title Change”
Now when I accept the connection to known hosts at first connection, the Putty window is embedded to RoyalTS every time.
No idea if this should stay as a default behaviour, but I’ll definitely take some time to bulk edit the Connections to disable this.