I can tell you what I did, Rabban. I am not sure which of these things, if any of them, made the difference.
When I was having trouble with small fleets, I had the original aliens, plus the Tribe, Swarm, and Order packs. I didn’t have the Nomads. Finally I caved into pressure from my sons and ordered them. As with my last upgrade of GSB, when I went to install, everything stopped working. I wrote to Red Marble, and they had me scrap the old game, download a new complete version, and delete my file of old ship designs and achievements (Library>Application Support>.com.redmarble.GSB). When everthing was running again, I noticed I had a new version number: 1.55.3. After playing the original game for a little while (to get enough honor to re-purchase critical modules), I went to try campaign again. Because I had a new program, I had to re-register it, and choose a new screen/user name (Lord Greenwood, if anyone cares).
So is it having all four extra races? is it the newer version number? Is it the new username? Something else? I have no idea. But it worked. Campaign is now incredibly difficult.