No matter what I do, my mouse isn't focused on Skyrim. When I'm in fullscreen, it works pretty well, but it acts like it's in windowed, cause if I look up too fast, the default windows mouse will show up. If I click when that happens, Skyrim gets minimized.

In windowed, it's impossible to play. When I look either way, the mouse exits the game and shows up on my desktop. I can still control my character, but if I click while my mouse is out of Skyrim, it'll just focus onto the desktop thus making the game unplayable.

I really want a fix for this because it's really stupid and wasn't in earlier versions of the game.

I did do a verify of the game cache (I have Skyrim on steam.) And I only have the HD mod and some mods involving the succubus summon. I don't know why the mouse is acting so stupidly.

That is the normal function of an application in windowed mode. I am guessing you have a non gaming mouse? Scratch that a non gaming or razer mouse:P
I prefer a 360 controller because even a good quality gaming mouse will fail hard in Skyrim. Aside that maybe the borderless mod is out of date and thus needs an update if you were not having the issue before.

But it happens in fullscreen too. And I don't have the borderless mod O:

What kind of background processes are running? Sounds like something is stealing focus or causing interference.

Ya in that case what Deaths Soul said above would be the next guess.

Go to the properties for TESV.exe and click on the compatability tab. Next tick the "Disable visual themes".

See if that works.

I usually have firefox and steam running. That's about it. Even if I close them, Skyrim still does this. I did the visual themes thing, but it didn't work except for the main menu >;O

Do you use Rainmeter or X-fire by any chance?

I don't have Skyrim but if its anything like other BGS games this is a simple potential remedy.

In the game's Configuration Settings file (I've no clue where Steam puts this) look for an entry: bBackground Mouse.
Make sure its set to: bBackground Mouse=0

Other considerations:
Do you have any unused gamepads/joysticks connected? Try disconnecting them.
Any unused IR Mouse/Keyboard receivers connected? Again, try temporarily disabling/disconnecting them.
How does your mouse connect? USB? Try a different USB connection. Shared connections/hubs can be problematic.
Run a dxdiag and check your DirectInput section for any issues.
Is your DirectX up to date? How about .NET?

Perhaps Weatherbug