Microsoft has just updated the following KB Article:
Windows Phone 8.1 users can install two versions of the Company Portal
Symptoms:
When Windows Phone 8.1 users try to install the Company Portal from the Microsoft Store in enterprises that manage both Windows Phone 8 and Windows Phone 8.1 devices, they may see the signed version of the Company Portal as an available app in addition to the regular Store version. This can cause Windows Phone 8.1 users to unintentionally install both versions of the Company Portal.
Full details at:
http://support.microsoft.com/en-us/kb/3038649