Yes that can be a very frustrating experience.  It sounds to me as if the entire Alliance team was all on D. If this happens its a tough thing to break at the end. The best way to break this is have the entire horde force run in as one unit...not trickle in which is usually the case. The entire force needs to stay on thier mount and actually run just past the flag and get into the area of the ones coming from the grave yard. This will pull the ones ahead of the flag back and you then have the chance to turn it. All easier said than done of course. Another trick when you are at the flag is to have many taurens trying to turn the flag with undead standing inside the taurens turning to. Makes it very hard to target the undead. 

The best solution of all of course is to not have the full Alliance team on D in the first place and that can normally be set up at the beginning of the game (Your results may vary on getting everyone to listen and work together). First thing. Let the alliance have SF. Dont ever take it or touch it. Set up roughly a 30 to 10 split. 10 on D at Galv and the rest pushing towards sp. Adjust these number to keep up with what the alliance does. Too much D by the horde however and you will stop them and they will all end up back at home keeping you from winning and frustrating you. Too little D and they will win the race (they have the advantage when it comes to taking the town). With a 10 man D team holding them up at Galv or IB if needed, while the Offense takes sh bunker, then sh gy, then bal then icewing bunker. This can usually be done while keeping them frustrated with the D team. If icewing bunker is going down and you have held them up successfully, at this point you can let them go. You are so far ahead you can win the race then. The only thing that would need to be defended is your hut in town. Let the alliance run free and it gets them out of their town and you can march right in. 

One final thing when you are in the end game and taking their bunkers. Be sure and keep a small D team roaming the map and take back the gy that they ninja. The alliance have a great trick to win even when it looks like a sure loss. If they take all the flags behind you while you think you have an easy victory. They will rush sp when you are trying to cap the aid hut. And you will suddenly find yourself in the cave back at the start.

I hope you have enjoyed my long winded answer.