When I stack a list of items Scapple changes the order of the items, often putting them in the reverse order.
This can’t be what is intended in the software design, surely?
I’m going to reply to this even though it’s years out of date because I was having the same problem and it took a while to figure out the solution.
Notes are stacked in the order you select them. Sometimes, depending on what notes surround the stack, it’s easier to select the notes with a lasso from the bottom to the top, but that will have the affect described by bimbogumbo - reorder the stack in reverse.
If you want to maintain the order of notes in a stack you have to select them in the order you want them. Having said that, if you select them at random, they seem to order randomly which I think is a bug.
UPDATE:
Definitely some strange behaviour in the way notes are ordered when you stack them. If one note is much shorter than the others for example, it seems to take that one out of order. As a workaround I’ve created keyboard shortcuts to do this:
Make Same Width
Align Left Edges
Distribute Vertically
Stack
Provided I lasso the notes from top to bottom and then do the above, I don’t have a problem.