My hunch (and it is just a hunch) is that your problem results from switching between a USB enclosure and direct connection of the disk. Some enclosures translate 512-byte logical sectors on the disk into 4096-byte logical sectors presented to the computer -- that is, the opposite of what the firmware in an Advanced Format disk does. I'm not positive, but I suspect that some enclosures do this only on over-2TiB disks. Both MBR and GPT partitioning schemes refer to data by sector numbers, so changing the sector size invalidates the partitioning data. Thus, if you prepare the disk in a USB enclosure that translates in this way and then try to use the disk directly (or vice-versa), you'll see errors because the partitions (and even GPT backup data) won't be where the computer expects it to be