Incorrect reporting of Partition sizes in Windows XP

Hi All, was wondering if anyone can help,
I have a 250Gb hard drive on a networked Windows XP Pro PC. The drive is partitioned as 116Gb and 116Gb C and D drives.
When the PC boots up, a startup script runs from the Host PC which loads up permissions, sharing etc.
When the PC has finished loading, the C drive partition is showing in "My Computer" as 5.3Gb with 180Mb free space (The D Drive partition still shows 116Gb).
I have replaced the HDD with a copy and this does the same thing.
The original HDD when removed and placed in external caddy and viewed on another PC shows the partitions are correct at 116Gb and 116Gb.
When viewed in "Disk Management", the top window shows the drive as 5.3Gb and the Drive information in the bottom window shows the correct partition sizes.
Also, I think the startup script loads a registry from the Host.
Any ideas?
 
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