It sounds like your flights are originating from USA? I wonder if this is the reason for this kind of behaviour bolded.
I wonder why there was a $600 difference if you did the upgrade during your booking online. Maybe a difference in tax applying to all sectors even though some sectors are not being upgraded?
It isn't confined to the US. It is also the case when you use the UK as departure point. As an example, if you select PE for LHR-HKG the price shown is £520 outbound. If you select economy then the price shown for PE is £600.
However, the overall price is the same as the Inbound for the first search is £520 but for the second it is £440, giving the same total of £1040