As I pointed out in another post a long time ago, you have to set "capture enemy ship" as the SECONDARY strategy. Give it a normal strategy like "optimal weapons range" for it's primary strategy. Then, when the target ship's shields are gone, it will switch strategies and board. Or at least it used to. I haven't used boarding in strategic combat for a long time now.
[This message has been edited by Baron Munchausen (edited 14 July 2001).]