I've also had problems with upgrades in the past. One of the business class perks, excepting BA, is being to select seats at time of booking. Also, because you have an individual booking you should be able to check-in online using your PNR number . I have usually needed to make several calls to sort out upgrades, book my preferee seat and obtain my PNR. Not great service, in view of the high cost. I have on occasion found I could book direct with the airline for considerably less than the JY quote. I appreciate there are admin costs, but some of the mark ups have been eye watering.