@Nico, it's funny, I hadn't actually tried anything yet, but for some reason my shake smelled a lot better this morning. And there's only one thing I did differently last time, so I'm wondering if that did something.
Here's my normal routine:
Fill my shake, drink it while working (this takes 30 to 60 minutes), fill it with soapy water directly afterward, clean it the next day.
Here's what I changed:
I filled my shake and when I started drinking it I changed my mind and wanted to eat something else. So I put my full shake in the fridge and left it there for a full day. The next day I drank it and did my normal routine again of filling it with soap-water afterwards and cleaning it a day later.
I really don't get why this would improve the smell, but it definitely is smelling a lot better now.