Photoshop CS5 Image Rotation Problem

Hi:
I have recently found out that I am having a problem with image rotation in CS5.  If I have a Background layer and jump the layer to duplicate it and then set the jumped layer to Flip Horizontal both the jumped layer AND the Background layer are flipped horizontally as if they are linked in some way.  The only work around that I could come up with was to duplicate the document, flip the layer in the duplicate and then combine the documents.  It works but what a pain.  As anybody else experienced this problem?
Herman R.

Charles:
My Background was locked and only the jumped layer was selected. 
However, the "problem" grows more intriguing.  I tried using Duplicate Layer rather Command J (is there a difference between these two??) and was pleasantly surprised to find that the problem disappeared!!  I then went back to Command J and still had the same problem.  To make a long story short, I went back and forth several time and then even the jumped layer worked as it should.  It was as if it had "learned" the correct behavior!  I tested it now ony several documents and all is fine.  Does this make any sense to you?
Herman R.

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