Kovid, I put the numeral zero in the box but it made no difference. The extra entries still showed up.
The odd thing is that these extra entries don't show up in the TOC window in Calibre's reader but they show up on my Touch. And I know they were added in upon the conversion as I checked the toc.ncx file both before and after the conversion using pdfxml inspector. The good thing is that I was able to delete these extra entries using pdfxml inspector but it's not the most convenient tool to use.
Any other suggestions?