Exchange 2016 CU3 was the 1st version of Exchange supported on Windows 2016 when it was released on 9/20/2016 [Exchange 2013 & 2016 quarterly updates out]. This was a minor update, biggest changes are the support for Windows 2016 and indexing from passive copies.

Today officially Microsoft posted:

Microsoft recommends that customers delay deploying Exchange Server on Windows Server 2016 until this update is made available.

Source: https://blogs.technet.microsoft.com/exchange/2016/11/04/update-on-windows-server-2016-and-exchange-server-2016/.

The issue surfaces as an issue with IIS, that causes W3WP.exe to crash, which leads to “instability” on that Exchange server and the DAG. The issues does not seem to appear on stand-alone servers. You will see event IDs 1003, 4999, & 5011 in the application logs relating to IIS issues. Per Tony’s post, see below, this issue is not directly related to IIS, but IIS crashes as a result of it. This it only appears on DAG members, which use Windows Clusters, so it makes sense it is related to clustering.

Tony Redmond goes into more detail here: Exchange 2016 to Windows 2016: No Thanks – At Least, Not for the Moment (11/4/2016)

One of the first public post about the issues was on the TechNet forums on 10/19/2016: Exchange Server 2016 & Windows Server 2016 Datacenter IIS AppPool’s constantly crashing. ECP/Powershell inaccessible.

The release notes for Windows 2016 have also now been updated with:

If you attempt to run Microsoft Exchange 2016 CU3 on Windows Server 2016, you will experience errors in the IIS host process W3WP.exe. There is no workaround at this time. You should postpone deployment of Exchange 2016 CU3 on Windows Server 2016 until a supported fix is available.

I will update this post as more info comes in or when a fix is posted.