Hi Lex.
I do not think this is a program error: I get it all the time, when my fingers move too fast.
Your first "click" needs to be Clone Stamp's initial "copy-from" location, and in which you must simultaneously hold down the "Alt" button (PC).
For further issues, delete your "CS3 Settings" folder under your Photoshop CS3 folder and re-start. The folder will re-build itself.
Michael