Hello all:
I've run into similar issues as documented in the original post above. I did 3 things that seemed to rectify my issue around different % completions for each scale stipulated during tile package creation. All of the changes below where made in my original map document that I used to generate the tile package in the data frame (i.e. map) properties.
1. In the Data Frame tab, I updated the Extent property to reflect my "Current Visible Extent".
2. In the same tab, I updated the "Extent Used By Full Extent Command" to Other. I specified the Extent as "Current Visible Extent".
3. I was receiving a warning upon analyzing my map document around a conflict between the data frame spatial reference and my layer's spatial reference in the table of contents (they did not match - the map document had many layers that were removed before creating the tile package). I do not think this warning impacts the completion of tile services, but decided to include it because I did correct it when I received the warning (I also wanted to be complete for others navigating to this post). Anyway, this was an easy fix and I navigated to the Coordinate System tab and imported my layer's spatial reference information.
After making these 3 changes, I saved map document, created the tile package and tested the TPK file with 3 different roles in ArcGIS Online: Administrator, Publisher, and a custom role I had setup for this specific purpose (although I did expect a privilege to be the issue, I wanted to eliminate variables). Each time I published the TPK file, ArcGIS Online reported 100% for each scale.
Hope this helps others who see this issue to resolve it. If Kelly's post is accurate, it seems like a check that the software should catch during the "Analyze" stage of this particular workflow (compare the initial extent with the full extent and report it to the user if they are not the same).
-=Steve