It seems that you are not able to assign multiple capabilities to Ground Forces, the option reverts to only the last selected when using the unit class design.
Scouring the rules posts it seems as if it was intended that units could have multiple capabilities. If that was changed I missed the post.
http://aurora2.pentarch.org/index.php?topic=8495.msg105824#msg105824Specifically:
At the top-right of the window is the Capability section. One or more Capabilities can be selected for the Unit Class. The Boarding Combat capability is required for a Unit to be able to board another ship. For all other capabilities, the Chance to Hit is doubled in the environment specified. If a unit has multiple capabilities, such as Mountain Warfare and Jungle Warfare on a world with a dominant terrain of ‘Jungle Mountain’, the bonus is cumulative (i.e. 4x to-hit in this case). Each capability selected for a Unit will increase the cost by the multiple specified. Some capabilities are only available for infantry units.
That is broken only allowing one selection.