I'm flummoxed by this. I think I need to confirm a few of your steps:
- With the Document Library panel, are you choosing Import Symbols… from the fly-out menu?
- Are you dragging any of these imported symbols from the Document Library onto the canvas?
Finally, are you saying that symbols are actually disappearing from the canvas, or from the Document Library panel (or both)?
This is surprising behavior to me, as I thought that symbols placed within the Document Library panel are saved within the document itself. In any case, one way to prevent this might be to copy the contents of your Libraries folder to your other computer, placing it in the corresponding folder. Oh, wait… maybe this is a CS6-to-CS5 issue? No, I don't think so… On a single computer, I'm able to create a file in CS6, and that file still contains the same symbols when opened in CS5.