Comment 4 for bug 556931

No we know exactly what the problem is, we just have no solution.

There are tons of .desktop files in /usr/share/applications that have 'exec=nautilus' so Docky will use *one* of those. Which one is probably based on alphabetized filenames or something, I'm not sure exactly but it doesn't matter. The point is it picks one and uses it, and the one it picks probably is wrong.