It appears that the export process from WP to Disqus did not complete for me for unknown reasons and I ended up with a partial amount of comments in Disqus. I looked at the instructions on this page http://docs.disqus.com/help/87/, and tried solution 2, which did not change anything, and then solution 5, which updated my WP database with the partial comments from Disqus!!! Solution 1 is not the issue here since we have the same version setup in another environment and it works. Solution 3 & 4 are not really options for us.
What should I try from here? Getting the backup copy of comments into my WP database, and then try re-exporting the comments from WP to Disqus? Anyone else has experienced the "missing comments" issue?