I too have this problem. As soon as I complete the "create an imperial faction" quest, the "unite the Empire" quest fails almost immediately.
To add to this, I just got one of the Conspiracy quests and it failed immediately - Reason "You couldn't complete the quest in time".
I am running patch 1.6.0
no mods.
Update - after patch 1.6.1 I reloaded an old save and tried again with the same results. Unite the Empire quest fails as soon as you get it with the "You couldn't complete the quest in time" reason. When you get the quest it shows no "Time to complete" field.
Any update on this? any chance it will be resolved in the next patch??