I have downloaded 4.6.1_12 and use it on a Windows 7 laptop connecting to RH 6.2 machine using Gnome. I do have the same type of problem.
I have set “ALT+<key above tab>” to move between windows. Whenever I switch away from NoMachine and back again I can’t use that sequence. If, e.g., an editor is in focus it types § instead of switching windows. If I then hit the same sequence again it happily switches window.