After finally finishing my model, I took it into blender to rig it. Ive rigged models before, and done it correctly, but for some reason when I try to use Forked extrude (along with x-axis mirror) to place the joints for the shoulders, the armatures just go wherever they feel like. Here's what I mean:

Before I hit Shift+E (Forked extrude) with x-Axis mirror on

After I do so. I mean what the hell. This isnt the first time this happened to me; and last time it did my rig turned out like stuff. Ive tried rotating the armature (in object mode) to make it line up with other axes to see what it did, and nothing changed. Right now it IS lined up correctly on the grid.
Im at a loss at what to try to get it working. Has anyone else run into this before and/or figured out how to fix it?