I recently created some partitioned queues from where I send and receive all the time. They\'ve run as non-partitioned in the past without any of my current issues.
From Service Bus explorer you can check these messages and the state of them, they might be in deferred state. To know more about deferred state read this.
"When a queue or subscription client receives a message that it is willing to process, but for which processing is not currently possible due to special circumstances inside of the application, it has the option of "deferring" retrieval of the message to a later point. The message remains in the queue or subscription, but it is set aside."