Construct itself likes to freeze when I run it. I wait about 2-5 minutes and it works fine, but that's an example of how it works differently on different systems.
I haven't upgraded myself to the unstable releases, however. What version are you using? Transitions always messed up my games in Construct. Instead, I just made my own transitions. For fade-to-black, just have it show a black box over-top everything and, once that box is 100% visible, go to the next level/scene/whatever. I know this just over-complicates things, but it works better. Now, if only full-screen mode had a workaround.
Why doesn't full-screen work properly, anyway?