I think I figured out the issue, it's to do with particle box size! When you apply an effect to the particle object, if you don't make the particles box size large enough then anything outside that box will be invisible/cut-off!
<img src="http://i.imgur.com/4iafrtz.png" border="0">
So the solution in my case is to make the box larger, but the question is, is this change intended or a bug?
I have a .capx with the "ripple effect" instead of the one I was using because it doesn't not come with the progam but gives the same result anyway.
.capx download