We've seen this error occur in multiple environments. Here's a workaround to address this problem. Attached is a powershell script that will itterate through all of the SQL registry tree's on a sql server and send the data back via the custom miniscan flag. Now with the inclusion of miniscan this script requires an agent to be installed on the device. Essentially, all you should have to do is run this script on a device and it will return the same results you'd get from the SQL Discovery Rule to inventory for your device.
To take this a step further, you can deploy this script in a distribution package and send it to your devices you need to get this information from for your reports.
Note: This script has been tested and works on 9.5, 9.6 or greater agents.