What you describe is possible. If your van has an Isolator then a failed or failing Isolator can allow the motor battery to discharge into the cabin battery.
2006 was around when Roadtrek was switching over from Isolators to Separators.
Has the problem reoccurred since replacing the cabin battery?
If you're able to post photo of what's under the hood up against the firewall I might be able to tell you if you have an Isolator or a Separator.
Isolator testing instructions: isolator sp1.pdf
Isolator troubleshooting: Battery_Isolator_Trouble.pdf