There is a known problem with the 2.4 release in that books without comments are generated as zero length files so that you get an error when you try and display the book details. However that affects both the XML and the HTML files so I am not sure that is the problem you describe. That particular issue has been fixed for the 2.5 beta 1 release which is available for download.
There is no known problem that affects just the HTML version of the catalog.
In terms of settings for most users the default settings tend to make sense, although the Stanza compatibility setting is required if you want download links that work with Stanza (as calibre2opds has to work around some Stanza bugs in OPDS handling).