Disable SUPER / WINKEY key in remmina
Comment moved to the answer because it seems to work.
Remmina 0.99.9 works ok for me, but I use it to connect to Linux via VNC only.
There is a bug that can be related: https://bugs.launchpad.net/ubuntu/+source/remmina/+bug/993432 --- is this your problem?
In that bug, one user says that clicking two times WINKEY rapidly solves the problem (open and close windows menu).