After you open the crystal bag, move the window (if required) so that is is not over the inventory window (if you are playing at a low resolution, you can move the inventory window partly off screen to make enough room). Then you can drag and drop crystals back and forth between the inventory and crystal bag. If the crystal bag window is in front of the inventory window, clicking on a crystal in the inventory brings that window to the front, so you can no longer see/access the crystal bag window.
