Did you clear the cache partition after the update? If that didn't work you may have to backup the phone with kies or smart switch and do a full backup and then do the dreaded factory reset .
We want to keep your apps from disappearing, tgs. Which device do you have? Were you able to try Ann154's suggestion of moving the apps back to the phone's internal storage?
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SD cards, in general are slower than the internal memory on the device if the launcher loads before the apps on the SD card do, they won't be seen in time to load onto your homescreen.