In the Border Battle at Deneb G-10 this week the Itani fleet had double of all the capships. Only one "set" of capships was in the mission group and only that group could be boarded. Capships that were not in the group would not respawn if they were destroyed, nor would they count against the score for the itani's(though that was hard to tell cause only a trident and teradon died).

http://www.box.com/s/8q6jjm377gdgbt2nfqxt
http://www.box.com/s/ufk693aujst42xagcrau
http://www.box.com/s/5gitv12pizea6qcera2o

EDIT: Can someone tell me how to make pics work in the thread so ya'all dont have to follow the links.

Thanks.
We're currently working on some Border skirmish problems that may be causing this.