Are you by chance running on MacOSX?
I'm having the same problem and have determined that eclipse is starting up with a current working directory of ${install.dir}/eclipse/Eclipse.app/Contents/MacOS which is where the actual executable is. I noticed that the workspace directory was not created where I expected it to be so I searched for it and that is where it was.
I modified the ant script to put the full path in for install.path but this seems to have caused other issues with null pointer exceptions when importing the sample project.