It is possible the disk drive is using MBR partitioning instead of GPT partitioning, which could result on size irregularities with disk drives over 2TB.
I would recommend performing a full test using Western Digital Data Lifeguard Diagnostics for Windows. If a full test and S.M.A.R.T. status test are to pass then the disk itself is healthy and re-initializing should correct the issue. After writing zeros to the disk (low level, deep-sector format), you will have the option to initialize the disk again.
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