Windows native backups makes SQL Server think that databases backup has been done
This KB isn't directly related but the quote in it is: 

MSKB2615182: Windows Server Backup May Fail Because of the SQL VSS Writer:


  When Windows Server Backup attempts to backup a disk volume, a Volume Shadow Copy Snapshot is created for the volume. When the snapshot is created any VSS writer associated with the volume is called.  


If there are SQL Server VSS writer backups being taken then you will see records in the MSDB.dbo.BackupMediaFamily table in the physical_device_name column. You might want to look into disabling the SQL Writer Service.

TechNet: SQL Writer Service