I love WinMerge. It has become one of the tools I depend on, especially for team work. You know how much some people hate cvs, so manual merging is always needed, and winmerge kicks butt for this.
 
However, I have seen that sometimes when doing a directory comparison, nothing happens. (Yes, I have all the thing in the "View" menu enabled.) It is instantly done, with no noticable disk activity. The "directory comparison" window does appear, but with nothing in it. Are you guys aware of this?