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"Filesystem Damaged" but chkdsk reports no issues


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Not aimed at you.  Most likely, it's logging "Error (3)" or similar when this occurs. 


Click on the "Settings" button in the toolbar and select "Scanner Settings". Enable the "Show advanced settings and information" option, and hit "OK". You will only need to do this once, from now on, it will always display this option.
Click on "Settings", and find the "CHKDSK" entry.  Click on it and select "Verbose".
Then clear the status on the file system for one or more of the disks, and start the scan again, until this comes back.
Then grab the contents of "C:\ProgramData\StableBit Scanner".
Note, this is "ProgramData" and not "Program Files".  This directory is hidden by default. 
Head to https://stablebit.com/Contact and attach the files there.


Could the volume be too big for the scanner to understand?


The file system scan is an API call to the same engine that CHKDSK uses.  It's essentially just a CHKDSK pass. 

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I want to use Stablebit Scanner, but have found myself going in circles with it.  No amount of chkdsks find erros but SBS will.  No matter what I do, can't seem to resolve these issues.  Even tried the newest beta. Not quite sure how to reset a damaged file system status so it's healthy again,

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If this is Windows 8, Server 2012 or up, make sure that you are NOT using the "/scan" option, as this skips a number of critical checks. 


That said, you can reset the status by double clicking on disk in question, clicking the ">" next to "File system health" and then clicking on the button with the green circle. 


If this continues to happen, consistently, let me know.

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