I once saw a case when file copied to pendrive had small patch of zeros where normal file had data. Is there a way to check whole disk for this kind of errors and if possible disable bad sectors ?

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Usually bad sectors trigger an Error while copying. Any way run disk check on the drive with bad sector repair oprtion & see the log:

chkdsk /X /R dive_letter:
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Alternatively, you can right-click on the drive on the Computer screen. On the Tools window, you will see an option to check the drive for errors. This brings up a dialog that allows you to optionally check for bad sectors.

Caveat: This works in Windows 7. I think it works similarly in Vista, but I'm not sure about WinXP.

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