Site searching spell autotargeting targets provinces that do not already have the path searched at all and do not already have two or more sites. If a capital only happens to have one site, it gets targeted, period. The mechanics do not make any difference between a capital and a normal province.
Most recent big thread on site searching
Older big thread on site searching
It's generally a good idea to do a search on a topic like this, but I suppose this is going to be in the FAQ since I get tired of rehashing the same things over and over again.