The thread number controls the maximum number of threads that may be used in a search. The automatic option sets this number internally depending on the size of the used HD space or the available processors (when you have Intel Core 2 Duo or AMD X2 CPU). When it is checked the slider on the right is grayed and no longer available.

The Fast start option is trying to optimize the program for better user experience during the first search. Try to turn it off and compare performance. If it is better you can leave it unchecked.

Index Searches option can vastly improve performance for frequently searched patterns. Maximum number of searches to index is 500.