I am having trouble following your description. Are you able to post a couple of screenshots to demonstrate the issue?
Also check the brush mode of your clone stamp tool in the options bar - is it set to normal ?
Hi Dave, I sorted this problem in the end - When you have the clone stamp tool selected there is a button in the toolbar at the top of the screen called "Aligned" - if you have this selected there will be a crosshairs slightly away from your tool which is where Photoshop is sampling from - this sample may not be what you want though so it is best to have 'Aligned' unchecked.
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The difference between aligned and not aligned is that with aligned checked the distance between the sample and the stamp remain constant even if you click to paint more than once. With aligned unchecked, every time you click to paint the sample goes back to the start position.
So in the two examples below I sampled on the centre of the D on the left block then painted in three separate areas on the right (not resampling)
First with aligned checked:
Second with aligned unchecked :
I hope that helps your understanding