I think I'm having the same trouble as the original poster, who's question wasn't really addressed.
In Logic X I'm finding that sometimes if a region is faded in and then faded out it's fine but when the fade in, for example, is changed to a speed up, the fade out will then stop working. Change the speed up back to a fade in and the fade out works again.
Am I making myself clear?
Fade in — fade out = cool
Fade in — slow down = fade in stops working
etc