How do I get rid of the annoying mRemoteNG lost connection popups that happen whenever an SSH session times out?
The popups actually come from PuttyNG. You need to change the putty options under tools->options->advanced. Relevant options are setting Session->"Close window on exit" to Always, enabling Connection->"Enable TCP keepalives" and setting Connection->"Seconds between keepalives" to more than 0.
Remember to save the PuttyNG settings as "Default Settings" in Session->"Saved Sessions".