Sounds to me like they're updating the baggage allowance display to properly consider who you're checking the bag in with (1 bag 50 lbs each on the outbound is consistent with an economy fare checked in with EI, whereas the return the silver wavier would be applied to allow +1 bag over ticketed allowance), and it just doesn't know what to do when the second segment is upgraded with an instrument as opposed to a fare. As far as EI is concerned when you check in with them you're still on an economy fare and you'd be entitled to the economy allowance since that is what is encoded in the ticketed fare.