There is apparently a compatibility issue between the old Mediascape framework and the new one, so if you do the update without a data wipe, your gallery/videos/music player will be constantly crashing, and fail to see pictures/video/music on the SD card.
I would recommend doing this update twice - first the default PC Companion update, and then a repair. This seems to clear up the problem, and I can now see everything from my SD card in the new framework.