So,
I discussed this issue in depth with SC when I was over there, actually to be specific I discussed it while devouring a rather excellent Reindeer - so you could say because of this Christmas is going to be slightly different now Rudolph is dead - I hope you are feeling guilty
This is a REALLY difficult one to solve, basically whenever the base is disrupted by something like a defence or if you are attacking it messes with the timing, I can't go into any more detail partly because I didn't understand it fully (there was wine involved) and partly because it's not public knowledge how it works. What I suggested would be to look at the timing differential and then compensate - i.e. if on average it's causing the timer to end 10% too late then adjust the time by that % - it's not a perfect fix but it would ease people's pain a LOT.
They felt that was a good idea - but I'm not the one developing the game so I can't promise anything - but I can promise that next time i'm with them i'll be raising it.
I do promise you that it's not:
a) a conspiracy to make you buy gems
b) any of the other conspiracies
It's just a really tricky one that causes issues for those who notice it, and none whatsoever to those who don't.