I have a similar issue. Cloning does not do anything. I am on the right (and at the moment only layer). There are no adjustment layers. I can set the cross with alt + click. But when I try to paint, the cross moves in the selected distance to my mouse but nothing is painted to the layer. When I change flow from 0% to about 30% it paints something. But with 0% absolutely nothing.
Affinity Photo 1.6.5.135
BTW: It would be good to have some kind of obvious feedback on what layer one is actually working on in order to avoid confusing situations and accidently painting on the wrong layer. However in my case it does not seem to be a layer problem at all. Looks like a bug to me... Please note, I am a beginner also, so I may be mistaken.