Global axes all messed up

Alright, I’ve been trying to figure this out for an hour and it’s driving me insane.

In 2.53 Beta, I’m modeling an object and I’m trying to mirror something along the x-axis using the duplicate/scale, x, -1 trick and it’s flipping the object along some weird axis that I can’t even figure out. So I try a mirror modifier with the same result, it’s mirroring along something I’ve never seen before. Turns out, the Y ans Z axes flip to the same exact thing if I put in a negative number for scale. What the hell is going on here? I’ve been using blender for almost 4 years and I’ve never seen anything like this.

EDIT: Seems to only be happening in object mode, but I’d still like to get it fixed so that I don’t have to keep reassigning origin points…

In object mode, select your model and try applying scale and rotation (Ctrl-A), but NOT location. I think Blender loses track of axes when you combine object- and edit-mode rotation and scaling operations, and ctrl-A usually sets it right.

Applying Location is weird in 2.5; it moves the object origin to the coordinate system origin. That doesn’t seem right.