You need to create a new strategy.
The defaults have garbage orders for the "shuttle carrier" type of ship. Which essentially means "don't get hurt" strategy.
When you add a new unit type (called, "XYZ" for example), the strategies get two new entries;
1) XYZ
2) XYZ Carrier Ship
You'll have to edit the default strategies.txt to include something for those two in order to get sane results
You can also delete your existing strategies and then create new ones in an existing game; the new strategies will have entries for the new unit types.
For reference, I had to have the following lines in GGmod's strategies:
Code:
Target Type 11 Name := Militia Carrier Ship
Target Type 11 Engage Distance := Medium Range
Target Type 11 Damage Amount := 100%
...
Target Type 15 Name := Ground Base Carrier Ship
Target Type 15 Engage Distance := Medium Range
Target Type 15 Damage Amount := 100%
...
etc