In private correspondence with a Panorama X user, we worked out that there is a bug in the Dock that causes problems when you drag a Panorama X file directly into the dock. At first it seems to work, but as soon as you save the file, the Dock forgets that it is a bundle and then just thinks it is a folder. So at that point you can’t re-open the file using the icon in the dock. When the system reboots the dock performs some sort of magic and then recognizes that the file is a bundle again.
Of course I’m sure you won’t want to reboot every time you save a file. Fortunately there is a simpler solution – make an alias of the database, then drag that alias into the dock. This works perfectly, even when you save the file.