The Dunov capital ships appear to have issues with auto attacking. It seems like they interrupt their auto attack when they use their abilities. But, it might be that they just have a bug in their auto attack. When I park a Dunov next to a structure and leave it to auto attack, there are very long gaps between volleys. If I keep right clicking on the structure to make the ship attack, the structure dies about two-three times as quickly (the Dunov attacks two-three times more often). I didn't explicitly test other capital ships, but it seemed like it might be occurring on the Kols, as well.