Mint is tricky with B6. On B6's website, you can't even book a Mint seat in an itinerary that includes a connection to a flight with no Mint service. In fact, even when you call B6 reservations, some agents can't even do it.

I know you are talking about a codeshare, but it may be the same limitation. Refer to the thread "Connecting Mint Flight/Mixed Fare Booking" about this. The bottom line, this may be a HUCA situation until you get an experienced agent.