I found a way to get around this...not sure if there is an easier way.
This usually happens to me if I make a build first, then revert it into an egg (especially when using a hatched Pokemon as a base). If you did this and are at the egg version with "0" hatch counter, here are the steps I took to fix:
1. Uncheck Egg on "Main" tab
2. Go to "OT/Misc" tab
3. Click on the Memories Button, then click save. This will erase/overwrite something in there that is creating the 0 hatch counter. (This only works once you've decided to make a "hatched" build into an "egg" build, and already checked it prior to all these steps.)
4. Go back to the "Main" Tab and re-check it into an egg again
5. Change the hatch counter (if needed) and set the Pokemon in a box. Then view it after you set it to see if the changes were fixed. You should be able to adjust the hatch counter now, and it will set accordingly.
I can't talk the correct terminology of the issue, so understand this is just a workaround I have found to be useful instead of re-making a build starting with the egg as the base. Good rule of thumb is to use an egg for the base of your builds whenever possible. Hope this helps!