Since the release of Exchange Server 2016 Cumulative Update 3 (CU3), which added support for installing Exchange 2016 onto Windows Server 2016 servers, there’s been a series of reports in support forums and blog comments about errors that customers are seeing.
Now Microsoft has acknowledged that there is in fact a known issue, and there is no current workaround for it.
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.
That’s all the detail that has been publicly released by Microsoft at this time, but the guidance is clear. You should deploy Exchange 2016 only on Windows Server 2012 R2 until further notice.
Update: the Exchange team has added some more info:
There currently is no workaround for this problem. Exchange Server will install on Windows Server 2016 cleanly and appear healthy until the first reboot after creating/joining a DAG. Customers should avoid installing Exchange Server on Windows Server 2016 until a supported update for Windows Server 2016 is available. Customers whose production environment is impacted are encouraged to replace Windows Server 2016 with Windows Server 2012R2 if they cannot wait for the update.
Update 14/12/2016: an update has been released for Windows Server 2016 to resolve underlying issues that adversely impact Exchange 2016 servers.