Wingzing I just plugged your barebones itinerary into the tool and was able to select all flights and price it up (came to just under 900,00JPY)
After I had put all the cities in, the tool was warning me that the second visit to Asia had to be under 24hrs. Once I selected the flights into and out of HKG, that warning went away.
So perhaps there is something else in your full itinerary that is causing the problem?
Ps Your itinerary does NOT violate rule 4(e)