Strange, maybe the VNC software you were using ?
(PS: I use one on which you can set the “grab keys”, to prevent using an existing shortcut).
Note that everything works this way for me, and faster than normal VNC !
In the domU I can use KB shortcuts/macros, the Fn key, etc.
I have several AHK scripts handling my own shortcuts, including one mimicking Unix-like GUI shortcuts (Alt+mouse to resize/drag, etc).
Ofc with USB PCI-PT, you won’t have any lags !
Maybe, or it could be the sector size/misalignment ? I’m no pro so forget the words.
There is a thread worth reading : Survey: CPU and VM boot time.
Somewhere in the middle, there is a discussion about sector size or sector alignment, 4k sectors stuff on SSDs, or something like that ^^