It's a bug. Support responded with the below information and workaround.
There is a known issue in the current Lansweeper version with custom registry scanning. More specifically when scanning multiple registry values within the same registry key, as is the case in your environment. A fix should be included in one of our future releases. We recommend checking our changelog for bug ID: LAN-9577 when a new version is released to make sure this fix is included. You can enable the update check in the Lansweeper web console under Configuration\Your Lansweeper License to be notified of any new releases.
You can find our changelog here: https://www.lansweeper.com/changelog.aspx
In the meantime, we have a workaround for you as we've discovered the root cause of the issue. Our developers recently made a change in the way scanned data is saved to the database during rescans. To reduce the overall amount of database transactions necessary. An incorrect assumption was made about registry key scanning here. This allows for the following workaround:
• Open CMD on your Lansweeper server as administrator
• Run the command below, correcting the Lansweeper installation folder path if needed:
"c:\Program Files (x86)\Lansweeper\Tools\ConfigEditor.exe" /showfeaturetoggles
• In the featureToggles section of ConfigEditor.exe, click Add
• Enter UseCompareDatasetsV2 with a value of 0
• Click Add, then click Save configs and restart service
• Afterwards you can rescan your assets and all registry values should get picked up again