Virus and NFTS vs FAT32

Is there a virus that can cause files do disappear from a directory. It seems on my old drive some files would just get bad or disappear completely. Many times my system would perform a disk scan at bootup when I never asked for it. When it runs it finds pieces of files and attemts to restore those sections. ? Is it a virus or an NTFS problem?
BTW in formating a drive should I create my boot partition in FAT32 or NFTS.
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Lee W, MVPTechnology and Business Process AdvisorCommented:
The first part of your question is basically corrupt files - where the disk has failed, the master file tables have gotten corrupt, and/or the computer has been shutdown incorrectly.  Windows attempts to recover what it can of these files and puts them in fileXXXX.chk files and dirXXXX.chk files.  Sometimes the data is readably - most of the time its junk.

In my opinion, you should go with NTFS.  It supports larger hard drives more efficiently, allows for security and on-the-fly file compression and in general is more robust than FAT32.  The one advantage to FAT32 is that it can be read by almost anything.  But there are tools  including the Windows CD itself, that can access the C: drive, when formatted NTFS and the Windows install isn't running well.

For a comparison of FAT32 and NTFS see

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And if possible, regularly take backups with the most important data.
What OS will you be running? windows98 = FAT32
With XP you have the choice
You hard drive could be failing. You might want to download the hard drive manufacturers hard rive utility and run a diagnostics against the drive.
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