Collector's Edition Borked

I have the Collector's Edition and I upgraded it to 1.11 (or whatever the current version is) immediately after installation. It worked fine at that point. When I downloaded and ran the three files that are on the www.galciv2.com/collectorsedition page, absolutely nothing was added to the game (I checked ship parts, custom portraits, custom race icons, etc.--nothing new). Unfortunately, much of the game was removed. Sandbox settings (such as No Tech Trading) are gone, enemy race selection gives "?" for portaits and has lost the randomization options, Autopilot Lines can no longer be displayed, homeworlds aren't named, autopilot targets have no ETA, and Neutrality Learning Centers can't be built, just to name a few.

Needless to say, this sucks... I'm reinstalling now, but is there any way to safely apply the Collector's Edition content, or should I go without?