Trouble updating fresh Windows Server 2008 R2

While preparing new template images for Microsoft Windows Server 2008 R2, after the first round of installing Windows updates this happened:

Windows Server 2008 R2 Stage 3 of 3 Failure configuring Windows updates Reverting changes Do not turn off your computer
After just the first run of installing Windows updates on a fresh Windows Server 2008 R2, some, if not all, changes needs to be reverted.

The same thing happened last week on a production server running Remote Desktop Services, and luckily that server recovered from this traumatic experience. I’m not sure which update/updates is/are causing this behaviour in the first place.

Update 2014-01-24

It seems a progressive approach is the key. Just let Windows decide which updates to apply at each step. You’ll cross the finish line eventually.