First thing you need to do is update photoshop using Help>Updates from within photoshop cs6 as many bugs were fixed and your still on 13.0
(not that what your describing is a bug, but version 13.0 had lots of glitches that'll drive you crazy when you encounter one)
Also, the global lighting may be different from one document to the next as you have Use Global Light checked in the drop shadow dialog
Layer>Layer Style>Global Light>Angle
See if unchecking Use Global Light makes any difference
I've been through changing the angle many times myself, but it's explainable:
The Global Light value does not get saved with the style.
R_Kelly has described the right approach. Save the style with the Global Light checkbox off and you should be good to go. This thread reminded me to go change a preset style I made that I use a lot to do just that, since when I'm using it I always seem to forget to change it. Hopefully neither of us will see light falling from the wrong angle again.
Thank you so much for your help R_Kelly that was exactly the problem, I had global light on. That totally helped me out at work.