I have scripts from 1.4 using the say for x seconds block. When ran in 2.0 the baloon doesn't always dismiss/
One circumstance that i can replicate is when i click on the “saying” sprite while the baloon is displayed. The respective sprite has a “when this sprite is clicked” handler script; the baloon is triggered in another script listening for a certain event on this sprite.

Do you have a link to the project that shows this bug?

While trying to replicate the problem with a smaller script, I ran into another issue. I will continue attempting to replicate my original reported issue.

The script linked below has two animals and two fruit sprites. The goal is to be able to draw a line from an animal to a fruit. You will see that in order to do that, i use a fifth sprite, which is largely invisible, whose pen is drawing the lines.
When you click on one of the animals the “cursor” changes to a tennis ball, my sixth sprite; if the tennis ball is dragged to one of the fruit, a line is drawn between the animal and the fruit. However, if i move the sprites around the canvas, the lines no longer draw where they should. I added some “debug” baloons, which pop up for 2 seconds, before and after the line is drawn.
This feature of goto worked flawlessly in 1.4 to my shock, as I didn't think you could use the goto block with a variable containing the name of the sprite where you want to go.
Oddly, if you chnage the costume of sprite Drawing to the soccer ball, things work ok.

http://scratch.mit.edu/projects/10179192