I'm a new user but I've also been having problems with the clone tool. What seems to be happening is when I hold done Control to select the area to be cloned, it creates two circles so I can only COPY from one circle to another (not across layers, or freely clone).
I've attached a screenshot showing the tool creating a carbon copy of the original image (on the left). The copy (on the right) is slowly being built up each time I use the tool. Obiously, if I try to 'clone' away from the original image it is just copying the canvas so it looks like nothing is happening.
I've also tried using the rectangle select to slect an area first, but this doesn't work at all (for me). The second screenshot shows the rectangle being used.
To use the clone tool, I'm holding down Control then left clicking to select then just left clicking to 'paste'.
I'm running Vista SP2 (build 6002) 64 bit and have .NET framework v3.5 Sp1 with the latest version of Paint.NET (3.5.1).
EDIT TO ADD: I've run pdnrepair.exe, which finished successfully but the problem remains.
Screenshot 1 showing the clone tool 'Copying' the original image
Screenshot 2 showing the clone tool with an area selected first