Move and Rotation Matrix is off its default axis

[LittleRainGames]

So I just used the Loft tool to make an object, and now when I try to move or rotate vertices (On all objects), they are all off axis. Instead of moving or rotating on XYZ, the matrix itself seems to be rotated. It was doing that with the face tool as well.

How can I make it go back to normal without restarting the program, or deleting my configuration files?

And also how can I change the matrix to a certain angle of my choice? I am seeing that it could be very useful while creating buildings that are off axis, especially if I make them normally, rotate them but then need to fix something later when its already in the scene.

Here is a picture. My little XYZ drawing is what it is supposed to be by default.

[LittleRainGames]

I just solved my problem, it is the working pivot as seen in the hierarchy window.

 But it still doesn't explain why after using the loft tool it rotated the pivot of every object in my scene?

Edit: Ok and I just realized, after I changed the working pivot, and then reset it, when I try to move or rotate the vertex it didn't reset the pivot for the vertex and it is doing the exact same thing. Even with Use working Pivot unchecked.

[LittleRainGames]

I actually didn't solve it sorry. It doesn't seem to be the working pivot, its only when ever I use Loft and convert it to editable poly, the vertices axis are all off. But the working pivot kind of answers my question, but how can I do it without the working pivot? While the working pivot does a very similar thing, when you want to move a vertex, the Axis gizmo is in the same place every time, instead of on the vert.

Edit: I just realized it also screws up after I set a working pivot, even if I reset it. I'm starting to think this might be a bug.