When I flew FCO-MAD-MIA last year, check-in opened up 34 hours before the first flight's departure and I was offered an upgrade to J on both sectors. The upgrades were available both on the app and in MMB on the website. Maybe try the app if the website failed to process the transaction?

BTW, on that occasion I paid for the upgrade on the MAD-MIA sector and immediately received a confirmation e-mail from IB with the receipt for the purchase. My credit card was immediately charged the USD 320.22 amount, and I was also able to select seat 7J in the business cabin. However, when I checked back in MMB five minutes later, the seat in the biz cabin had disappeared, and I was seated back in PE. EF showed the flight as J8 C8 D5 I2, so there still were 8 J seats available.

So basically a glitch in IB's systems had caused the downgrade to be voided, although my card had been charged. I contacted both IB's cust. service (useless) and IB's twitter team, who were very competent and forthcoming. They tried to get my upgrade reinstated, however because the flight was now under airport control there was nothing they could do. They suggested that I take my upgrade receipt to IB's service desk when I landed in Madrid and try to get the upgrade processed by them . By the time I landed in MAD the next day, according to EF the flight was now J1 C1 D0 I0. I walked into the Velazquez lounge at T4S, showed my upgrade receipt to an IB agent at the entrance desk, and asked her if she could manually process the upgrade and grab the very last remaining business class seat for me, which she quickly did.

So all was well in the end, but there's lots of things that can go wrong with these upgrades!