@HaQue,
HaQue wrote:format it with NTFS with something like 2 x 1.5Tb partitions or 3 x 1TB and you should have no issues (if the drive is ok of course)
That approach (of keeping the
partition size below 2TB) would only work if the problem was related to the partition size. Your suggestion would still allow the OS to (try to) store data and filesystem metadata beyond the 2TB LBA of the drive. If (as
fzabkar suggested, and I agree) a plausible explanation is related to addressing limitations of the USB enclosure, and in that case the partition size is not relevant.
Can you explain your theory of how limiting
partition size, while still allowing all 3TB of the drive to be seen and used (or at least try to be used) by the OS, will prevent the OP's problem? Perhaps you've spotted something in the OP's story which others haven't...
@ptzelepis,
If the theory previously explained by
fzabkar is correct (and I've seen the same problem in the past, with similar results to yours, so I agree with it based on current data), then the problem is your choice of USB enclosure for use with a 3TB drive - not all of them support >2TB drives. Either you need a USB enclosure which properly supports a 3TB drive, or you need to limit yourself to using a maximum of 2TB e.g. by not having any partition (and therefore any filesystem) use any of the drive above the 2TB point, or setting a DCO or HPA to limit the reported drive size to 2TB (the latter two can only be done using specialised utilities with the drive connected via SATA - I don't recommend these solutions for novices, but include them just for completeness).
Of course if
HaQue's different theory is correct, then the solution is different too.

I can suggest tests which would help to confirm which theory is correct, if you want that, but they would
permanently erase the data on that drive. Your choice