I'm having the exact same issue. It would appear to be related to the active scanning, since the number is going up on its own, and at a rate that can't be explained by regular logon activity. Furthermore, I can get a machine to scan properly using lstrigger or manually calling lsclient from the machine, but it will show back up on the "WMI Access Denied" list soon enough.
The error being shown for me is: Access is denied. (Exception from HRESULT: 0x80070005 (E_ACCESSDENIED)) COMPUTERNAME ()
Nothing has changed in my environment other than the version of LS I'm using.