We have seen a handful of cases where a player's Command Center has become stuck while changing Factions. In these cases the timer and the gold cost to finish will disappear from the user interface, and it will appear that there is no way to complete that process.
If your Command Center is stuck in this state, just click the use gold option. You will be not be charged any gold, and the process will be completed immediately.
We are working to resolve the underlying cause of this issue now, but in the meantime this work around should prevent you from being stuck without your Faction Bonus.