After setting up Qemu/KVM and VNC and fixing cursor positioning issues (with the -usbtablet option), I had an annoying issue of the VNC viewer (TightVNC in this case) sometimes missing mouse clicks. You would quickly click on a button and icon and nothing would happen. If you hold it for long enough, it will eventually register. I don’t want to be holding my button for a second to make sure every click regsiters though.
After fiddling around with the options, I finally found the culprit. The option inside the VNC viewer “Emulate 3-buttons (with 2-button click)” seems to be the cause. Turning it off seems to make my mouse clicks reliable. No idea why though.