Originally Posted by onlySIA

No idea, maybe you booked into one of the more flexible classes of PE and so when you request to upgrade they assume you want a similar level of flexibility, whereas the low J price is for Business Lite?
Or may be a computer glitch due to the outbound and return routes being different, such that a new booking is priced correctly whereas upgrade is priced as two one way trips (assuming the 5500 fare you are seeing is for identical routing).