Microsoft is still scratching its head over a mystery that has some users reporting that settings within Windows Vista’s Automatic Updates feature are changing on their own.

The issue arose after this month’s Patch Tuesday when users began reporting patches were installed automatically and their systems rebooted even though they had specifically disabled automatic installation. The glitch was first reported by the Web site AeroXperience, which said users had their machines rebooted automatically at 3 a.m. the day following the patch download.

It is unclear whether the glitch also affects other versions of Windows, namely XP, and Microsoft is not saying. It is also unclear whether corporate users tapping into Windows Software Update Services (WSUS) were facing similar issues.

What Microsoft is doing is collecting log files from affected users, according to a recent blog post by Nate Clinton, program manager for Microsoft Update. But so far, Microsoft has not come up with any definitive answers.

Clinton said the log files show that none of the Patch Tuesday updates made any changes to Automatic Updates settings. He said all the logs collected show that the machines were already set to “install updates automatically” before the Tuesday patch release.

Automatic Updates itself does not seem to be at fault either.

Clinton also made a point that the client software for Windows Update does not change AU settings without a user’s consent.
“We are continuing the investigation, and as I have more information I will update this post,” Clinton said on the Microsoft Update Product Team Blog.

The Automatic Updates glitch follows on the heels of user complaints that Windows Update was conducting updates on user's machines without their knowledge or approval. Microsoft said the function was a normal part of updates and apologized for not being clearer about how the feature operates.