Out of curiosity. Are two snapshots created even when creating the snapshot manually?
With backup applications this behavior is not unusual. The first snapshot is created for the VM to write the changed data while the snapshot/backup is active, and the second snapshot is created due to the backup software attaching the base virtual disk to the backup host/proxy as "Independent - Non-Persistent". Once the virtual disk is disconnected from the proxy the second snapshot will be discarded and then the first snapshot will be committed to the base disk.
The CBT information should not be reset in any way, but updated according to the changed data during the backup.
André