I'm not a Stardock guy, but the boxes were distributed by a different company. Stardock didn't have the original distribution rights, but only picked it up a few months (6 months?) after the game debuted.
For the boxed versions, StarDock didn't get a penny's revenue. StarDock first offered it on their site at the $20 price tag, as opposed to the $40 Retail price that it originally hit retail establishments for in the US.
As a result, they don't really support the boxed versions. That, plus they don't necessarily have control (or information) about the code that went into the versions besides what they're selling--not that different, but different enough that support can get very expensive in a hurry.
You'd need to go to the original game publisher (1Cenega, maybe?) for support on the boxed versions...