If your using the HD spec as a reference for amount of space you're expecting, then you need to read up a bit on what happens when you format the hard drive. There is a difference between non formatted space and formatted space.
If this is not the case, take a snippet of your main HD and post it on here. We can help you and narrow it down from there.
There is no difference between a formatted or unformatted drive. The "difference" you see is the misrepresentation of the volume size by the OS because its (the OS) is using the incorrect suffix to state the size. However, if the OS did infact use the correct suffix, then the volume stated would be correct.
Example:
WD 640GB HDD contains 640,132,575,232 bytes (more then 640GB by 132MB).
Windows misrepresents the total size as 596GB.
GB=1000^3
It should actually state 596G
iB.
GiB=1024^3
640GB = 640,000,000,000 bytes
596G
iB = 639,950,127,104 bytes
596GB = 596,000,000,000 bytes
596GB =/= (596GiB = 600GB)
Since your using Windows, simply goto "Windows Explorer", right click on the actual drive itself (for example ( C: )) and choose "Properties". The screen that opens up will give you the correct total space in bytes just above the pie chart. You can simply use the first group of number(s) before the comma and add 'GB' to that to see what your actual total drive space is (which would match whats stated on the HDD itself).
Now if your actually "missing" HDD space because of other issues (hidden partition? incorrectly partitioned? system backups?), what the others have stated are things that can help you look into it.