I was connecting to a physical display using 6.2.4 free client on Windows and the same version server on Linux.
Weirdly, I was running Chromium on xcsrv in rootless mode and had the exact same problem. I’ve had various keyboard problems on this Windows machine with different versions of VNC too. I guess it’s possible there’s some problem with how Windows 7 is handling the keystrokes.
I have since tried out x2go and it seems to work much better for my purposes. I can run individual applications rootless. My understanding is that NoMachine only does that on the paid versions. X2go is also more responsive for me. So I don’t think I will be pursuing this bug further.