Since I did not see this topic posted in "problems", I will address how I fixed it here.
I had the same issue with hot buttons on a large object that were supposed to pulse in a staggering way 6 times each upon entering the scene and then repeat the same action after the scene has been idle for a certain number of seconds. I found that not all of the hot buttons would repeat, especially if you had clicked on them already. There was nothing in my triggers that indicated a reason for this, since I was only changing opacity and not hiding them. They were all identical, except for where they fell in the timeline (fractions of a second differences). Also, the player was freezing up the first few times after I upgraded.
I solved these issues by resorting to animated gifs. Each hot button is an animated gif, instead of making the software do the animation. It now runs faster and has totally reliable animation.