If the URL that should be indexed but is not, is present in the siteidx?.url file, this means that a page pointing to it has been found, but that the URL did not match the index criteria. This can be the Depth or the MaxFiles options.
A common error comes from the robots.txt file on the web server that excludes a directory from indexing. Check out it's contents in order to find out whether this is the problem. If yes, you can always ignore the robots directives by adding Robots=N option to the asearch.cnf file.
Note that Alkaline 1.3 uses a new .urt structure for urls and it gets much more difficult to find out if an url is indexed or not. There's a way to find out why a particular url has been excluded, run Alkaline with the -exv command-line option.