It was mentioned in the Beta 2 Change Logs that starbases are now autopinned. I believe this applies to all starbases in a game. Including your enemy's. If a scout enters an enemy system, the system automatically shows up in the empire tree, with the enemy starbase pinned.

Please verify if all starbases on all sides are to be autopinned.

Also, starbases seem to have the 30% Damage and 100% antimatter removal of leaving enemies applied before construction of the base is complete.