Last night I was playing a fallen spire campaign my first shard recovery went well, but when I sent my survey ship to begin the colony ship recovery the survey timer didn't start. I tried sending the ship away and bringing it back, as well as rebuilding it in the system where the scan was needed, neither worked.
Here's the savegame if you can see something wrong, I'm going to start a new game with the same map and settings to see if I can reproduce it.