Does your project contain symbolic links? The TODO bundle uses the common path of all files in a bundle. If the project contains files in /var/logs/ and files in /Users/soryu/Projects/foo the common path is / and the TODO list will search the whole harddrive, that is /.
Soryu - you are right, and my surmise was wrong. I had a symlink to a file that was causing the whole harddisk to be searched. I've amended that and now the search works fine.
And thank you Haris, for setting me on the debugging path.
Bruno