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Ditto what Clare said:  CS6 or even CC is almost the same as CS4 in this regard.  Probably the best way to get to the bottom of this is if you could post some screen shots showing the sequence of events that leads up to this problem. 

That being said, your statement about the "no pixels selected" warning suggests that your initial setting for feathering  of your selection tool is  much too large.  Set the feathering to zero on your selection tool to zero before you start, and see if that helps.

Tom