I have created an object and duplicated it 20 times and numbered them from 1 to 21 as the order they are created. First I have stacked all of them at one place so that only the last one can be seen.
[Edit]
Then, the top object is moved to a different location, creating enough distance to the stack so that all other objects fit in between.
Now when I click on distribute centres equidistantly vertically selecting all of them keeping one of the object far below and all rest at the same place, then order of distribution gets haphazard.
This happens even if the number of objects is 17 also, but gets perfectly ordered distribution if the number of objects is 16.
The distribution order does not hampered if the objects are placed at different positions vertically, they will then distribute according to their position order.
My Inkscape version is 0.91 and I installed from the PPA [http://ppa.launchpad.net/inkscape.dev/stable/ubuntu trusty main] and my OS is UBUNTU 14.04 LTS 64-bit.
I am attaching here the inkscape file example.svg for better explanation.
And here is an attachment of PNG file (the output of that svg file) for quick look at it.