The repair hulks warp in when you kill x number of cubes.
There is definitely something screwy with it though but most of the time it is completing because Fed players are killing the hubs making it a win for the Klingons - hence all the reports of "it ended but I didn't get credit" which is because the Feds won the game for the Klingons hence did not get credit for a victory.
The simple recipe for Fed victory is....
1) Scan 8 nodes to advance to stage 2
2) Kill cubes untill hulks warp in
3) Kill Hulks
4) Prevent Klingons and/or other Feds from killing the nodes before you kill 4 hulks.
Thats it, simple to explain......almost impossible to achieve when random Feds keep killing nodes.
Note to Cryptic: Nodes should not be hostile to Fed players, make them friendly and you have fixed this problem