When I run the Generator, the results always shows 27 pages indexed no matter how many pages are actually in the sitemap.xml file. You already have my website generator login credentials.

from what I see some pages are skipped due to the Exclude URLs setting. One of the lines is defined as "?", which means that any page with "?" in URL is not indexed and crawled, i.e. pages linked from that page will not be found either.
Nothing to do with the ? exclude (that was your recommendation for me to use anyway). The problem seems to have worked itself out, and I believe it was on the server end.