My first thought is that maybe you have a complex document, and are doing something like sampling all layers, but cloning into a layer below an adjustment layer. Or that maybe there's an optical illusion at play (it's happened). But it's impossible to know given what you've said.
Your expectation that the Clone Tool should not change tonality is generally on the mark, but this is a case where the specifics matter.
It might be helpful if you'd take and post screenshots showing the problem, and especially showing your Layers panel and anything else that could be helpful (ideally, the whole screen). That might prompt further questions or a jump right to the answer.
Thanks Noel. I experimented on a blank new image, so I was just working on the Background, with no layers, and the clone tool worked fine. But when I went to one of my illustrations (which have many layers) and worked on just one layer, the clone tool overlapped the colour. I've attached screenshots of both.
Judging from the checkerboard patterns in your layer thumbnails, it looks like you're painting on layers with partial transparency.
Cloning partially transparent pixels over other partially transparent pixels makes them increase in opacity. This is true with all versions of Photoshop, going way back. I just did this with Photoshop 6.0.
Perhaps you could separate the layer into its pixels and maintain the transparency separately in a mask, though this is going to mean that you may have to do some extra work to get the layer to look right. Or you could remove the transparency entirely and set your layer to Multiply blending, which if it's substantially white will darken the places you paint.
Thanks Noel. I never had this problem before so maybe it's something that's a default with the later versions. There must be something else I can do as your solutiion sounds complicated! (I'm not that good at PS!) When I did cloning on the new image in red, I only had the red at 70% transparency, not 100%, and it worked fine. so I really don't know what the difference is between my illustrations and the new image.
Your test with red was on a Background layer, which is always 100% opaque.
One quick question, that might not play a role in what you are seeing:
Do you have an Adjustment Layer, that is affecting the Layer, where you are doing your Sampling and Cloning? If you do, just turn that Adjustment Layer OFF, do your Sampling and Cloning, then, when done, turn that Adjustment Layer back ON.
Good luck, and if you have no Adjustment Layers, just ignore my suggestion.