I just wanted to add that after I upgraded from 1.5.1 to 1.5.3, my permalinks quit working with 404 not found error, and also when you clicked on my comments box you got the same error. After reading this post I checked the files on my server and saw that the htaccess file had vanished. Fortunately, I had followed the instructions on upgrading here and first copied all the files to my own computer, so all I had to do was upload the htaccess file and all works again!
