Hmmm, I just did some testing.
As I mentioned earlier, bounding box coordinates are stored as ratios in the XML. So for example, if you have an animation with two frames, frame1 is a 32x64 image, and your bounding box coordinates are (0, 32), (0, 64), (32, 64), and (32, 32) -- eg, the lower half of your sprite, then the XML will store these values as (0, 0.5), (0, 1), (1, 1), (1, 0.5). Frame 2 however is 32x128, twice as tall. If you right-click and apply the original bounding box to the entire animation, frame2's bounding box will be *twice* as high as frame1's bounding box.
Here's a picture to clarify:
It should be noted that image points are stored internally the same way.
Obviously this is exaggerated for purposes of explanation, but I'd wager it can lead to potentially subtle bounding issues when you factor in things like toggling pixel rounding, and if a frame's height changed from an even value to an odd value.
I think people get burned when they don't use fixed dimensions (or they do on import, but then let Construct crop transparent edges). Then they setup a single bounding box on the first frame of some given animation in a sprite and apply that bounding box to an entire set of animation's frames.
I just did a quick prototype using the SingularEntity (aka Controller also has animations) of Mario. I can walk, run and jump on flat and sloped surfaces without any problems at all. However, I was very careful to import all my animations as a fixed dimension sprite sheet. Seems to work perfectly. I'll post it up later if anyone's interested.
@MultipleChoice, If you still happen to have the old original project with the jittery animation, I'd be willing to take a look at it and see what's going on with it.