If the url contains port numbers like "http://howtoforge.com:80/index.html", lighttpd will lookup the database with the port number. To ignore this, use

"SELECT docroot FROM domains WHERE domain= SUBSTRING_INDEX('?', ':', 1);"

as sql statement.

You also can add a new column into the database table with the port number to separate the docroots for different ports. 

"SELECT docroot FROM domains WHERE domain = SUBSTRING_INDEX('?', ':', 1) AND port = SUBSTRING_INDEX('?', ':', -1);"

Greets, Sannny