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.
This happens because when Windows Phone is enabled through the Configuration Manager console, the signed Company Portal is added to the managed software list just like any other app. The signed version of the Company Portal is compatible with both Windows Phone 8 and Windows Phone 8.1, however the Store version of the Company Portal is compatible only with Windows Phone 8.1. This is why only Windows Phone 8.1 users experience this issue.
For all the details and a resolution please see the following:
KB3038649 - Windows Phone 8.1 users can install two versions of the Company Portal (http://support.microsoft.com/kb/3038649)
J.C. Hornbeck| Solution Asset PM | Microsoft GBS Management and Security Division
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ConfigMgr 2012 R2