Please test the following scheduler configurations:
- Open Malwarebytes' Anti-Malware and click the Protection tab
- Click on the Scheduler button
- Please make sure that the Scan tab is selected and click the drop down menu next to Frequency and select Once
- Click the drop down next to Type: and select Flash
- Check the following options:
- Perform scheduled scan silently from system account.
- Save log file regardless of user settings.
Set the time of the scan to occur sometime in the near future so you don't have to wait too long.
Once the scan completes, please check the following location to see if a log has been created there:
C:\WINDOWS\system32\config\systemprofile\Application Data\Malwarebytes\Malwarebytes' Anti-Malware\Logs
Please post back with your findings.