A useful tool:
MD5 & SHA Checksum Utility
by: Download.com staff on November 30, 2009
Raymond Lin's MD5 & SHA-1 Checksum Utility is a standalone freeware tool that generates and verifies cryptographic hashes in MD5 and SHA-1. Cryptographic hash functions are commonly used to guard against malicious changes to protected data in a wide variety of software, Internet, and security applications, including digital signatures and other forms of authentication.
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MD5 & SHA-1 Checksum Utility is free to download and use, though Ray accepts donations from satisfied users. At a mere 57k, his checksum tool is about as small as a useful, functioning utility can be in this age of bloatware, and even more so considering that it's certified to work in Windows Vista and 7.
One would use this to verify that any copy of a file is that same as the original. So if one were to suspect that making a copy of a file made some very small change, the utility will sport the change, but can not locate the cause of the change.
As for Windows XP, not are versions behave the same way. In fact, a XP version may change behavior in a short span of time. The has been documented extensively and is also my personal experience. There is not easy or quick way to find out how and why XP changes its behavior. No verifiable reason has been given.
Do you wish to pursue this as an academic experiment? MS no longer supports XP, so we do not expect they will be of any help.
EDIT: Microsoft does admit XP can have strange b behavior.
Unexplained Windows or software behavior may be caused by deceptive software Notice how they shift the blame. 
Nor do they admit there are other reasons for storage behavior; namely updates that modify Windows XP.
