The issues were first reported by Exchange MVP Jeff Guillet:
With CU6, admins can no longer use the Exchange Admin Center (EAC) to create new Office 365 mailboxes, move mailboxes to Exchange Online, or create In-Place Archive mailboxes. Admins either need to use the Exchange Management Shell (EMS) or logon to the Office 365 Portal to perform these actions. In addition, when you click the Office 365 tab it normally takes you to the Office 365 signon portal so you can manage your Office 365 tenant Instead, it opens a new website for the Office 365 marketing page. These are huge problems for most hybrid customers and there’s no mention of this anywhere in the CU6 release notes.
Jeff’s current recommendation, which I have also updated my CU6 article to include, is to not deploy CU6 if you are a hybrid customer.
I expect Microsoft to publish an article soon regarding these bugs, but with a long Labor Day weekend ahead of us I wouldn’t expect anything sooner that Tuesday. I do expect that CU7 will correct these bugs. In the meantime, I recommend that hybrid customers do not deploy CU6 at this time. If you’ve already deployed CU6 in your environment, there’s no way to roll back.
At the time of writing there was no update on the Microsoft Exchange Team blog other than a brief note in the comments of their CU6 article.
Update 2/9/14 – KB2997355 has been released with a fix for this issue.