slacktom
Sorry to dig up this old post, but I'm working on just this problem. I bought the Quake 4 Special Edition DVD which comes with Quake 2 and both Mission Packs. I tried copying the files as you did, and had the same problem. It turns out that the problem is a missing gamei386.so library, which is needed in each mod directory for the it to work correctly.
Can someone who owns original The Reckoning and/or Ground Zero expansion CDs post a list of all the files and directories on the disks. Then I can make an updated installer that works for them as well as the Quake 4 DVD.