File copy/transfer to PC issue. MTP?

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http://forums.androidcentral.com – Unrooted S3 here with Jelly Bean. When copying all files and folders from Internal SD, not everything is being copied to the computer. Out of 33 total folders, only 20 were copied, another time 30 were copied, and another time only 5 were copied. This happened even with the external microsd card. Any idea how to fix this? (HowTos)