Comment 4 for bug 1323006

Hm looking some more, gnome-settings-daemon runs syndaemon with -t which is 'disable tapping and scrolling'.

The moving the mouse is still allowed in that case, hardware buttons too. But scrolling and using tap to click shouldn't be.

Keys used with modifiers are ignored by syndaemon too, it's passed by gnome-settings-daemon.

Is this what you're experiencing?

Also sarvatt notes that using the same key repeatedly disables things for a second, then enables it for a second, then disables etc etc.