automatically? Just because the Flash Drive is plugged in at start up?
Digger
If anyone has seen the Windows message at boot that a drive needs to be checked for consistency and a flash drive is plugged in, be aware that hidden protected files might be written to that drive. You need to go to folder options and uncheck the box to hide protected OS and hidden files. You may find a folder called "FOUND.000" which will contain the results of a chkdsk that, if the drive is a smaller one, might be occupying enough space to be worth deleting.

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