There is a configuration setting that can be used to control the queue name:
You can add it to your service configuration files like this,
<Setting name="AzureQueueConfig.QueueName" value="yourqueue" />
Or add it in app.config like this:
<AzureQueueConfig QueueName="yourqueue" />
PS: Define endpoint name should work as well, can you reproduce the issue in a small sample and file it as an issue on https://github.com/nservicebus/nservicebus
Thanks, Yves