I'd guess (from the name of your binding) that the reason this is happening is that you're binding to a CollectionViewSource (that wraps a collection).  This class is a proxy that WPF uses that includes (amongst other things) the selected item of a collection.  Obviously if you're sharing this collection between two comboboxes, you're also sharing the selected item.
If you set ItemsSource to something that's not a CollectionViewSource, the control will automatically wrap it in one.  So, my suggestion would be to bind directly to a collection instead of wrapping in a CollectionViewSource - or, alternatively, create two CollectionViewSource instances, one for each ComboBox.