Cs6 is saving all layers into one. Is there any way I can retrieve the layers? Help!

I switched from CS5 to CS6 and now everything that I save, when I go back to it, it is merged into one layer.  The layer box is checked in the save dialog.  The one thing that I did do was make a pdf of of the file also in the save as menu.  I have done this a ton of times before in ealier versions and my files were never merged.  Can someone please let me know what is wrong?  I have put in hours of work and now I can't edit anything.  Can I get the layers back?

I have noticed that this only happens after I save as a pdf in a separate file.  First, I save the file in a psd format to keep my layers, then I save as a pdf to show clients.  My other files that were saved in psd only, still have the layers.

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