Hello,
when you use the Engine Friendly Mode, the number of threads is limited to 2 and the number of results to 50. The process of query is intentionally slowdown in order to not harm the engines and to make the query more similar to human input.
When you have checked the option "Check for exact URLs" the program will count only exactly matched URLs like
http://www.mydomain.com/page1.html. If the option is not set, the program will count all pages, which belong to your domain
http://www.mydomain.com/.
Best regards