I rated yours yesterday (just commenting so I can see where I'm at on the list) - but yeah, I know exactly what you mean about having last minute problems in Unity! I tried to implement a neat lighting effect when the items are ported in mine, and it completely broke the game! I still haven't figured out why. Had to backtrack and use a particle effect instead, but it happened with less than a day to go and really made me anxious!
Viewing post in Congratulations! Now, who wants me to rate their game? :D
I think the problem I had was with an animator. I had placed a 2d light with the intensity turned to 0 on an object, then used an animation to ramp the intensity up when triggered. It caused a couple of objects to spawn in weird locations. I think perhaps it was resetting the transform location even though the location was never animated? Like I say, weird last-minute problems, heh. Fortunately removing that effect fixed the problem...