I am using Hayden's V0.3 fix, with the newly patched Skyrim. I have noticed there are some mouse glitches. In the load screen, the mouse pointer was on screen, and it seemed disconnected from the Skyrim mouse pointer. After Alt-Tabbing a few times, the two synced up and I was able to control the in-game pointer to start the game.
Also, I have noticed that in conversations (and other times) I lose the ability to choose options with the mouse. I can still rotate my view slowly while in conversation, but the mouse pointer is nowhere to be seen.
I have had the second mouse issue prior to the patched skyrim, and I am not sure it is related to the fix tool, just thought I would mention it. Not game breaking.
The center monitor is the only place the mouse pointer shows up. However it is also on the monitor to your right, you just can't see it there, the pointer goes out of view on the right monitor. The monitor to your left you can't move the mouse on to.
This is probably what you're talking about?
In other words, if you drag the pointer off the center screen to the right it will disappear but it won't stop till it hits the right side of the right screen. Its there, you just can't see it.
This is probably because the menus and what not are offset by one monitor width from the left side. So the mouse is active on both the center and right screens, you just can't see it when it on the right screen. Only on the center.
If the mouse disappears or goes 'out of sync', mouse back to your left till the mouse is back on the center monitor and you should see the pointer again. You had control of it the whole time :)