That sounds like I haven't labelled them right!
So that part of the transformation panel controls dead space/cutting out images so only valid pixels are visible.
If it uses Per-Tile, then a bounding box of each tile will be calculated - so if it changes shape or volume then each tile will be offset slightly.
For sequential animations, try "Use Automatic Largest". This should look through all your images, and find the biggest bounds of the entire sequence. Imagine if you stack up all your images on top of each other - that's sort of how this will be calculated.
Additionally make sure you're all set to look at the correct calculation - the default is Alpha, but if an image doesnt have Alpha this can get confusing.
I will try to make the default behaviour/factory default for this to be Use Automatic Largest; I've just noticed my default settings here default to Use Per-Tile. I'll also throw on a (?) section for this.
I think Per-Tile is probably more of a sprite-packing kind of system, and Automatic Largest is more for animation sheets (which is what it will mostly be used for!)