Something weird is going on here.
I have a document that's defined as 400x400 px, 100 ppi. The grid is set to 100x100, and there are four boxes to a side, so that matches up.

The problem is, the dimensions given for the vector box don't match up. Tool Options - Geometry claims that the vector box is 100x100 pixels, but the box takes up a little more than a square and a half of the grid on a side. The ruler agrees with the vector box, and claims that the entire document width/height is just under 300 each.

What the hell is going on here?

I'm running Krita 2.6.2 backported from Ubuntu Raring Ringtail (13.04), in case that helps.

EDIT: So right-clicking the ruler changes the measurement unit. That's good to know. Apparently the ruler that agrees with the vector box is measuring in points, whatever those are.

My best guess is that Tool Options - Geometry is actually measuring the box in points (pt) even though it says "px" after the number.
It doesn't make much sense, but I can't think of a better explanation.

EDIT2: Odd that you can't set the rulers to measure in pixels, though.