I've figured out how this happens.

SPOILER ALERT

For some reason not doing the Brotherhood quests involving convincing Madison Li to return the to the BoS , and the subsequent quests involving the construction of Liberty Prime doesn't allow you to progress further than Spoils of war quest should you choose to tell the Brotherhood Of Steel about the Beryllium Agitator when the Institute INITIATE the quest.

However following the Brotherhood quests involving Liberty Prime it works as it should and you can progress to Ad Victorium. (PRIOR TO GETTING THE MISSION MASS FUSION FROM THE INSTITUTE)

I dont know if this is an actual bug, or just the game punishing you for not randomly talking to everyone, but i had no data in my inventory suggesting i need to talk to Eldar Maxson to get these missions. It was just blind luck i went there after my initial trouble with this quest (involving the institute path).

I had to reload my save game right near the institute meeting and convince Madison Li to come back to the BoS.

I think this needs looking at Bethesda.