Minecraft 14w06b, Minecraft 14w07a
Windows 7, Java 7u51
Presumably this is a problem with all commands using cubic selectors however most visible with /kill. Using /kill alongside x,y,z,dx,dy,dz to define a cubic search area does not kill the next entity in-line. (Whether or not the sorting is done by distance or creation time.)
I've done a bit of testing and it seems that the result depends on the chunk the entity is in: /kill is misleadingly processing which entity to kill next on a chunk-by chunk basis within the search area, rather than the search area as a whole. Chunks closest to 0,0 are processed first.
Simply put: the list of entities is not being sorted by absolute_distance / creation_time before returning the first item.
To reproduce: spawn several entities diagonally across several chunks (3 or more chunks). Use /kill with a large square box (x,y,z,dx,dy,dz) that covers all chunks, as well as c=1 to only kill 1 entity. Notice that as you enter the command over and over, entities per-chunk outwards from the origin and not in the order of distance/creation.