I have an Asus g74sx dual-booting Ubuntu and Win7 via Wubi. My touchpad and usb mouse work perfectly in Windows, but behave abnormally in Ubuntu; if I just use the touchpad, everything works fine, but if I try to use a USB Mouse, the mouse will function on the window that has focus, or on the desktop, but refuses to change focus unless I right click on the window's titlebar repeatedly until it snaps to. The odd thing is that this behavior also affects the touchpad; it has the exact same issue while the USB mouse is plugged in. Removing the USB mouse will return the touchpad to normal. I have tested this on Unity, Gnome-shell, Gnome Classic, and Enlightenment.
I'm a Linux newbie, so this may be quite a ways off, but its almost as if Ubuntu is not interpreting my touchpad as a touchpad; rather, it thinks its a proper standard mouse. This is also confirmed by trying to install Synaptiks for multitouch support; the touchpad is indeed Synaptics powered but Ubuntu doesn't recognize it when trying to install that app from the Software Center. If it matters, the USB mouse is a Cyborg R.A.T. 7 wired mouse, and performs flawlessly in Windows. I can also confirm this issue occurs when using a Logitech MX Revolution wireless mouse.