We suggest clearing your Studio One preferences.
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Quit Studio One
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Click Start and type %appdata% [Enter] to open the Roaming folder.
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Open PreSonus/Studio One 4
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Copy the contents of the folder to a folder on your desktop for use as a backup.
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Delete all files and folders except for the user.license file
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Launch Studio One 4 and reconnect the ATOM.
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Start an entirely new session for testing your issue.
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If the problem still exists, please feel free to copy your settings files back over from the backup you created in step 4.
*If you are missing any Sound Sets after doing this, simply go to Documents>Studio One>Sound Sets and double-click one of the files.