Half a drive being taken up by?

If you are running Windows platform, you might want to check the System Properties to see if you have backed up system restore points.

Personally I would go into the data files select a group of them and right click go to properties and narrow it down starting from there. Also use the disk management utlity and make sure the disk is partitioned for the whole drive and not half.

its windows 2003 server so no restore points

@pdantro
"when I search the drive using a drive space tool "

I have a tool I use to view files called "diskspace"

The drive is not paritioned, I already checked that in disk manager

Do you use RAID array in the server? If you have one 300GB and second 600GB drives in an RAID1 array, you will have only 300GB of storage.

I can check but will windows will always show you the usable not the overall (2xdrives)

system drive is physical, drive in question is on a SAN

"I have a tool I use to view files called "diskspace" "

Does it have the ability to show you the drive space being used by folders in which you have no permissions as well?

I would check another utility to be safe.....

TreeSize Pro (has a trial available)
http://www.jam-software.com/treesize/

Here's a list of some other freeware disc space utilities:
http://www.techsupportalert.com/best-free-disk-space-analyzer.htm

Personally, I've used WinDirStat before:
http://windirstat.info/

Also, be sure to run the utility as Administrator if you have UAC turned on.

Please provide a detailed description of the server setup.
Does the "600 GB" data drive have quotas enabled?  It might indicate that the user with which you logged in, only has 3GB left on that drive.
If you look at the properties of this "data drive" what is being reported as its size/capacity?

I have tried the utilities you mentioned I have diskdata and I own treesize, this is what I using to check, also there are no quotas

What is the configuration of the server?  Brand, model, RAID? Diskmgmt.msc what does it show?
What else is on the system? What services does the system provide??
run chkdsk on the data drive or appropriate alternative.
How large is the block size?
run
fsutil fsinfo ntfsinfo <driveletter>:
This will output something like this:
NTFS Volume Serial Number :       0x
Version :                         3.1
Number Sectors :                  0x00000000061a7926
Total Clusters :                  0x0000000000c34f24
Free Clusters  :                  0x000000000068fe67
Total Reserved :                  0x00000000000007d0
Bytes Per Sector  :               512
Bytes Per Cluster :               4096
Bytes Per FileRecord Segment    : 1024
Clusters Per FileRecord Segment : 0
Mft Valid Data Length :           0x000000000d62c000
Mft Start Lcn  :                  0x00000000000c0000
Mft2 Start Lcn :                  0x000000000061a792
Mft Zone Start :                  0x000000000042a120
Mft Zone End   :                  0x000000000042a140

You likely have larger values for bytes per sector, cluster and per filerecord segment.
You may have created the partition for a condition that is different from what ended up.
i.e. the data files were geared for large files, while the reality is that you have many small files. Create a new file on the data drive with a single character in it.
Check the properties of the file, what does it report for the size on disk? 4kb, 8kb, 16kb, 64kb, 128kb?
A partition has space and a maximum number of files that can be created in this space.

As it's Server 2003, the space could be used up by Shadow Copies. If Shadow Copies were enabled with no limit, then it can slowly use up all your drive space.

View this link to see how to check which volumes have Shadow Copy enabled, and how much space is allocated for use:
http://www.shadowexplorer.com/documentation/windows-server-2003.html

More info of Shadow Copies for Server 2003:
http://blog.benday.com/archive/2009/04/30/23223.aspx
http://www.petri.co.il/whats_shadow_copy_on_windows_server_2003.htm
http://www.petri.co.il/how_to_use_the_shadow_copy_client.htm

no shadow copies, I could run chkdsk but this drive is located on our SAN can I still run chkdsk? there are no partitions its one big drive, here is that output
NTFS Volume Serial Number :       0x3e58c58458c53c01
Version :                         3.1
Number Sectors :                  0x000000004affc073
Total Clusters :                  0x00000000095ff80e
Free Clusters  :                  0x00000000017ebcff
Total Reserved :                  0x0000000000000100
Bytes Per Sector  :               512
Bytes Per Cluster :               4096
Bytes Per FileRecord Segment    : 1024
Clusters Per FileRecord Segment : 0
Mft Valid Data Length :           0x000000000650c000
Mft Start Lcn  :                  0x00000000000c0000
Mft2 Start Lcn :                  0x0000000004affc07
Mft Zone Start :                  0x0000000002d8fec0
Mft Zone End   :                  0x0000000002d982c0

creating  a one character file has the size of 1k

You have 17ebcff clusters free which should reflect that you have 95+GB free.

The "size of file on disk" is 4096 bytes.

How is this SAN 600GB provided to the server:
Is it via iscsi/FC connection seen as local drive or is it mapped?
can you post the image from diskmgmt.msc (please do not post a bitmap file please use the jpeg, png, formated image if possible)

its fiberchannel, I am running chdsk right now so when its back up I can provide a screenshot

Data drives while meaning the same to all, has different uses, user data, database data, etc. What is yours being used for?
Are you running the analysis of chkdsk or was a repair needed which you are running now?

Try running chkdsk /f

chdsk did not do much, I ran it with the /f option, whether its  a database drive, application drive or just a storage drive data is data and I am missing about 248GB which is not appearing

no shadow copies
no page file
no hidden drives
single drive

This appears to be more than a 50 point question.

This page has 11 suggestions for possible missing space:
http://www.dslreports.com/faq/9623

Two of them not yet mentioned on this thread are the Norton Recycle Bin and Alternate Data Streams.

I answered my own question

What was the third party program?

commvault

Did you try "vssadmin list shadows"? Just for curiosity sake.

On several occasions I asked what services the server provides. Having this information might have led experts familiar with the app to ........