Why does TreeSize Free show different size values than Windows Explorer?
Differences to the size shown in Windows Explorer can occur because the free version does not take all NTFS-specific features into account.
Features like Alternate Data Streams (ADS), Deduplication (Windows Server 2012 and above) or recognition of hardlinks are not evaluated in TreeSize Free. The personal and professional edition come with an option to explicitly analyze these extended NTFS features, which may make the results more accurate.
Starting TreeSize Free "as administrator" will show larger parts of the disk that cannot be accessed by "normal" users.