Hello, sfgreg. I\'m the author of KTrove, maybe I can help.
It sounds to me like things got a little confused when you ran the script under two different users. I never tested for this condition -- the script was a quick-and-dirty affair for me to solve an immediate problem I had.
I would try completely undoing everything KTrove did (you may have to do this manually) and retrying it after you chmod /mnt/card to your user id. It\'s late right now, and this is a only guess.
Re: the 5600, I don\'t have one (this script was written prior to its existence), and so that is compeltely untested as well. It shouldn\'t forget about the links it made, though... that\'s very odd behavior that smells like a bug.
I would be thrilled to hear the results of using this under such conditions. If anyone needs more detailed help (looking at you, maybe, sfgreg), please do email me at the address listed in the doc file.
I haven\'t been maintaining KTrove as I switched to the OpenZaurus OS, which handles cards properly and renders KTrove unecessary. I am interested in repairing things that are wrong with it, though, and I\'m happy to help where I can.