The mesh does have a parent frame (when exported as a .x file that is), but it is a simple rotation to get it from Blender to DirectX's coordinate system, which I already account for.

The root frame again does have a transformation matrix, when exported as a .x, but it again looks like a rotation, and if I use that instead of the identity matrix with the Calc functions, it just rotates the bone affected vertices and makes it even more wrong!

What reference frame (axes) system are you using in your app? Right-handed or left-handed? Which axes is "up" in your system? How do you create your view and projection matrices?

If you're using a left-handed reference frame, the root frame transformation from the x-file is more than "a simple rotation," it's a transformation between two different reference frames. It's likely a scale and rotation. It would be suspicious for that frame transformation to be applied to a mesh in a frame hierarchy. Normally, DirectX exporters in Blender have exported a root frame with the right- to left-handed transformation (Blender to DirectX), and everything (including the frame containing the mesh) as children to that root frame. In a couple exporters I've used, the transformation is a rotation about axis ( 0, 1, 1 ) followed by a scale of ( 1, 1, -1).

What version of Blender are you using and what DirectX exporter are you using in your comparisons?

Also,

I'm pretty sure there is a keyframe matrix for each bone

If you're having trouble rendering correctly, you should know what data you have. Those are things you have to check in your debugging efforts. If you have garbage coming in, you'll have garbage going out.