disks needs to be checked for consistency

[FallingStar]

i'm running w2k and run Konppix from the cd on this computer also. i save the setting and other stuff on this same drive. people recoment to covert it to fat32 as it work better with Knoppix vs ntfs.
After I convert from NTFS to FAT32 by using Partition Magic, Every time I boot, I started to receive the following:

Checking file system on C:
The type of the file system is FAT32.
One of your disks needs to be checked for consistency. You
may cancel the disk check, but it is strongly recommended
that you continue.
Windows will now check the disk.
Volume Serial Number is 3F85-7401
Window is verifying files and folders is completed
An unspecified error occurred

It will not let me run disk defragment also. Run virus check many time, but nothing come up. I don't think it have anything to do with virus. I have one drive and one partition on this laptop. any idea how i can fix this issues without a fresh install?
Please advice

[fingers99]

There may be a tool in XP to reformat a drive fat 32. Alternatively, you might try mkfs.vfat from the knoppix disk.

But if you only have one partition on the drive, then you've almost certainly trashed your Windows install: I'm pretty sure you can't non-destructively re-format ntfs to fat 32.