Ross
I suggest that you follow vendor recommendation and apply this fix in your dogfood system as described in:
http://technet.microsoft.com/en-us/security/Bulletin/MS13-061
“For administrators and enterprise installations, or end users who want to install this security update manually, Microsoft recommends that customers apply the update immediately using update management software …”
With one modification if I may … “You should test it on non-production system first”.
It seems that there is a fundamental flaw in the process as this “tiny” patch in no way should result in such a mess. Also, I understand that CU approach is under review. Yes pushing on prem customers to update every 12 weeks is not such a great idea after all.
In my opinion for all on prem, unless you have no choice stay with what works, or go to Office365 and relax.