I know you're probably aware of the bug that packs recent upgraded designs on the quickbuild and governor screen. This one may be a result of that:

I go to update the ship building on the governor screen. I've upgraded my ship class two times. So all three generations of it are showing. I've figured out now to go to the bottom one when it has the same name listed three times. So I update all my planets to build the brand new version of the ship with fast engines and everything. I leave the screen and check a few planets. Sure enough, they're building the new version.

After a dozen or so turns, I noticed that the planets were still churning out the old version. So I went back to the governor screen, and they were still set to the new one. The planets were all set to build the new one (every single one of them), but they were still pumping out the old version. The old one had speed 4, the new, speed 7. Then I went back to the governor screen and it showed one planet was now building the old version again and all the others were still building the new. Yet, no matter which one they were set on, every single planet spit out the old one. And every time I tried to set it right in the governor screen, it showed in the quick builder and ship screen that it was the newest version, but spat out the older one every time. Edit: I'm using the brand new patch.