I believe that this process creates points in the order that the source data is encountered - if you select 100 objects to create points from and they were defined in an entirely random order then the points created will follow that entirely random order.
Different data sets have different requirements of course - what would you like to see (numbering from Lowest E,N to Highest E,N for example (while that will work with this data - if the Square was rotated 20 degrees that would not work any longer for example - please give us your ideas of how "Numbering Should Work" or at least the options you would want to see and I can add it to the list of requests in our system.
I could see
1) Lowest E,N to Highest E,N
2) Lowest N,E to Highest N,E
3) Lowest Station, Offset to Highest Station, Offset (Left to Right)
In this data set - to get a numbering that works eg (1) above, you could output to .CSV (p,e,n,z,d) and then sort the data in Excel based on Easting or Northing etc. and then apply numbering as you want it and then re import the data (not ideal but an option).
Let us know what you would want to see in different scenarios and we can review
I will take a look at your data and let you know if I can suggest anything else
Alan Sharp