The problem seems to occur when the terminal is losing focus, no need to switch desktop.
is this ever going to get fixed? it's really annoying. gnome-terminal 3.18.3 Linux Mint 18 LSB Version: core-9.20160110ubuntu0.2-amd64:core-9.20160110ubuntu0.2-noarch:security-9.20160110ubuntu0.2-amd64:security-9.20160110ubuntu0.2-noarch Linux fur 4.4.0-21-generic #37-Ubuntu SMP Mon Apr 18 18:33:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux -jake