If OP is booked JFK-SIN on SQ 25, this is considered a flight with 1 segment, but two sectors due to the "technical" stop in FRA.
In theory, if one wanted to upgrade FRA-SIN only, this may fail in this specific case as the booking is JFK-SIN and FRA-SIN segment (not sector) does not exist in the OPs itinerary.
This may all sound a bit odd and technical, but I could imagine this to case a problem as normally through pax to SIN from JFK need to upgrade the whole segment (meaning both sectors need to have availability) and the price is JFK-SIN upgrade price and not FRA-SIN as OP is not booked FRA-SIN - still with me

.
Anyways, worth a shot to call though and also look out for the SQupgrade bids (cash).