Pistons are weird. Let me rephrase that: redstone is weird. It never behaves how you would expect it to, consistently. This is especially the case, however, with pistons.
Here's one example:
As you can see, the redstone lamps transfer power in a normal manner (solid block receiving direct power will power the adjacent blocks indirectly). The pistons, on the other hand, behave a little strangely. The first extended piston is powered directly, so it extends. The piston below that one is receiving power indirectly from the block that the redstone is placed on (the lamps behave similarly if you take away the middle lamp). But where the heck is that bottom piston getting power from?
Apparently, pistons can receive power diagonally, or from two blocks above. It was considered a bug for a long time, however, it has since been marked as "Works As Intended". There's a more specific bug report here as well.
Even adding a block in between the redstone and the piston doesn't fix it:
So how do you fix this? Well, that depends on your intended design. If you're going where I think you're going, and going for something similar to a zipper elevator, you actually don't need to worry about this; the zipper design works despite the fact that pistons are activated 2 at a time. Otherwise, you might have to adjust your design, since no combination of blocks and redstone will power just one piston in a vertical tower of pistons. It all depends.
This is due to the South-East rule. Despite a lack of mention in that page, this quirk does affect redstone. What's happening is that the dropper on top receives an item from the bottom dropper before it's instructed to fire when the comparator is on the north or the west sides of the droppers (opposite to what you said). When the comparators are on the east or south sides, the redstone power is cut before the top dropper is instructed to fire for the last item.
But it's more complicated than that. It's not just where the comparator is placed in relation to the dropper, but also where the rest of the redstone is placed. I've set up the same elevator, but mirrored, and it no longer emptied the top dropper.
My suggestion would be to either use a different item elevator, or find which of the 8 versions is going to work best for you.
Best Answer
If you have multiple signals moving down in parallel, your best option is probably circuit C from http://www.minecraftwiki.net/wiki/Redstone_Circuits#Vertical_transmission. If this pattern is staggered 1 block apart on each successive line, adjacent lines should not interfere with each other. This circuit has the additional advantage that the signal can be extracted at any height.