I'm using v3.2.1397 with default install options. Even though logs are disabled by default, they still get created when there's an error or other reasons.
Even though I never enabled logs, Synchronize It! continually makes the C:\wndsync-log.html file.
If possible, can you move the default location to its own program directory and not C:\?
With default settings SynchronizeIt! should write report file on unatended runs only (with /auto). Is it your case? If you disable logging, will report file be updated?