I have this problem as well. Debian 9 with standard Gnome 3 desktop and Remmina 1.2.0-rcgit-29. The terminal window disappears constantly, but afaics only if I have moved to another workspace. Beyond that I'm unable to reliably reproduce this. I did a strace on the process during the disppearance and there was nothing obvious jumping out.
Btw. the old, similar bug Christoph was referring to is here: https://github.com/FreeRDP/Remmina/issues/274
