This makes sense to me. IIRC there was a thread a while back that provided inforamtion that the file for a AM redemption is not supposed to be able to accept a FF number (although people report being able to do this at the airport) as the AM redemptions are not supposed to earn any mileage regardless of the actual fare bucket used (although YMMV).

If you cannot add your FF number to an AM reservation, it makes sense that you would not be able to use your eUpgrades (for yourself or nominee) as I believe that the key field is the Aeroplan number field.

You might have luck trying to upgrade your reservation at the airport if you can add your FF number at the airport and standby for an upgrade.