Start with a clean index - remove all siteidx*.* files. Run Alkaline with the -exv command-line option. When -exv is specified, all urls found in documents will show on the console with a reason why they are being indexed or excluded from indexing. In 99% of the cases, this option helped identify one of the common configuration problems described below.
If the url is present, but was excluded - a reason should point you to the right options to add to the asearch.cnf file. Typically, a document with query arguments (parameters after the ? sign, such as http://www.server.com/foo?bar+name=value) requires the Cgi=Y option. Documents of a particular type or extension, such as http://www.server.com/foo.php, require the ExtsAdd option. In this case, ExtsAdd=php.
If the url is not present, look for HTML errors in the document that links to it. Alkaline doesn't tolerate html errors. You can use Alkaline to parse an html document by using the parse command-line option. For example, asearch parse http://www.vestris.com/ .