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I am experiencing file system corruption problems, such as lost clusters, cross-linked files or invalid files or directories

Explanation: While performing routine file system scans, errors are being detected on one or more disk volumes. These errors are usually lost clusters or cross-linked files. Compression errors on compressed volumes are discussed here. The disk itself otherwise works OK although a handful of files might be corrupted; if the disk is corrupted to the point of unusability, or if its contents appear scrambled, look here instead.

Diagnosis: A small number of file system problems is normal on just about every PC, depending on what kind of operating system and software you are using. In particular, lost clusters are common because any time an application crashes or there is a power outage, in fact any time an application is interrupted, it may leave behind partial files that show up as lost clusters because the file was never completed properly. However, finding large quantities of lost clusters even when scanning regularly, or repeatedly finding problems like cross-linked files or invalid files or directories, can be a signal of a more serious problem.

Note: A lost cluster is not the same thing at all as a bad sector (which is a physical disk problem, not a file system problem); see here for more on those.

Recommendation: You may want to try all of the following items:

• Make sure you thoroughly scan your disk for viruses, using an up-to-date virus scanner. Corrupting the file system is a popular game with viruses.
• Make sure that you are using the correct type of disk utilities. Using a disk utility not designed for Windows 95 on a Windows 95 system, or using one not aware of FAT32 on a FAT32 volume, will cause the program to detect "errors" that don't really exist. They just don't properly understand what they are looking at because they are out of date.
• If the problem recently occurred after installing a particular piece of software, it may be that program causing the corruption. Some applications can be buggy, and especially if they crash a lot, they may leave partial files and other file system anomalies lying around. Try not using the suspect application for a few days if possible, and see if the problems go away.
• Make sure that you employ proper shutdown habits. No PC running any version of Windows should be shut down without following a proper shut down procedure.
• If you are using Windows 3.x, look for old stray .TMP files in the temporary file directory (which is often specified with a "SET TEMP=<directory>" command in your AUTOEXEC.BAT file) and delete them. These files cause system problems sometimes if allowed to accumulate.
• Check for resource conflicts. These can cause files to be corrupted.
• You may have an instability problems with your operating system installation. Look in this section for more; you may want to try reinstalling the operating system. A recently-changed driver may be the problem.
• If you have recently installed bus mastering IDE drivers, these could be causing the problem. See here for more and try uninstalling them if possible.
• You may have a real problem with the disk that is causing the difficulty. In my experience it isn't too typical to find repeated file system problems without a real disk problem manifesting itself in other ways but it is possible. Troubleshoot the disk here.

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