Discrepancy between availble space and capacity on external HD

Disk Utility report (Consistent with Finder)

Mount Point :   /Volumes/partition2
Format :    Mac OS Extended (Journaled)
Owners Enabled :    No  
** Number of Folders :  10

Capacity :  1.9 TB (1,900,231,068,160 Bytes)    
Available : 1.9 TB (1,899,390,058,496 Bytes)
** Used :   841 MB (841,007,104 Bytes)**
** Number of Files :    55

sudo zsh;

du -hs *(D)

744K    .Spotlight-V100
0B  .Trashes
4.0K    .fseventsd

I am unable to recover those 841 MB. I have tried reformatting but nothing changes.

I noticed this issue after copying 2 files to the external drive and deleting them. I didn't pay attention to those stats before doing that but I suspect they were the responsible what's happening. Their summed sizes were at least similar to these 800 MB (I can't confirm if it's exactly the same as they were since deleted).

It's a new external hard drive and I need to know whether it's working properly. I have no experience with those and I don't know if I'm simply missing something obvious.

UPDATE 1: Trying the 1 pass zeros erase in Disk Utility (as suggested by @IconDaemon)

UPDATE 2: After the 14 hour process, there are still 841MB used. I can live with that but I fear this may accumulate.

UPDATE 3: Repair Disk

Verify and Repair volume “partition2”
Starting repair tool: 
Checking file system
Checking Journaled HFS Plus volume.
Checking extents overflow file.
Checking catalog file.
Checking multi-linked files.
Checking catalog hierarchy.
Checking extended attributes file.
Checking volume bitmap.
Checking volume information.
The volume partiton2 appears to be OK.

It didn't solve the problem.

UPDATE 4: I ran the WD Drive Utilities' Complete Drive Test and no bad sectors.

UPDATE 5: Reformatted to FAT - 2.2MB Used. Then tried Exfat - 9MB Used. HFS+ again - 850 MB.

Maybe it's just the case that HSF+ needs 0.05% of the drive to work as @IconDaemon pointed out. Alternatively Disk Utility is using some inefficient process to do the formatting.

Solution 1:

Try using Repair Disk in Disk Utility to fix any disk anomalies, or run fsck -fy / in single user mode.