I was in a similar boat. After many attempts to get this fixed with SE I was told the Onion Helm while a CE item was it's own code and not the same as the CE game code. Because of this I ended up with a service account with the Onion Helm and a service account with my other CE items. You might be seeing something similar. Maybe she had a regular account with just the Onion Helm code added to it and not a full CE game code.
I still have the huge 1.0 CE physical copy boxes, one for myself and one for my wife. She definitely has 1.0 CE cause im the one who bought them at the store, installed them on our computers, and registered them to play. I'm going to have to open a ticket it seems to try to get this fixed :/