Since pinkie, items are reverse-ordered in the launcher menu :
if in configuration dialog i have apps A B C D, the main icon will be A, but in the menu there will be (from top to bottom, my panel is on top of the screen, but it's the same with panel at the bottom of the screen) D C B.
For me the logic would be : if panel is at the top of the screen, have (from top to bottom) B C D, if it's at the bottom (from top to bottom too) D C B. The order from A to D should be consistent, whether the panel is on top or bottom..
In any case this changed since 4.4.x..
I'd say the most logical stuff (for fixed an free panels, and for horizontal and vertical panels) would be to have the “first” entries (the ones defined first in the launcher settings) to be near the icon, and the “last” ones, to be far.
That means the order needs to change when a (horizontal) moves from top to bottom, or when a (vertical) panel moves from left to right. Or the opposite. This means the menu has to know where it stands, which may not be the cas atm, or not a good idea, or whatever :)
Anyway, it's the way the menu plugin is actually managed, so I guess it's at least consistent.
Not too hard to fix, will look into this.
Committed in revision 28387.