After applying a Microsoft update to Microsoft Outlook, the Auto-Import Folder Configuration information for the Integration for Microsoft Outlook can be lost. If this is the case, the integration tool bar and ribbon are still displayed, and ad-hoc importing is successful, but user-specific Auto-Import Folder Configuration options are missing.
This issue is caused by the installation of Outlook-specific updates from Microsoft. These updates cause a new sub-directory to be created within the original installation directory (in a ClickOnce deployment, this is the location of the deployed integration on the client machine, not on the deployment server). After the update, Outlook uses this new sub-directory as the location of the user.config file, which contains the user-specific Auto-Import Folder Configuration information. However, the new sub-directory does not contain the original Auto-Import Folder Configuration information for the user. Instead, a new default user.config file that contains no customized settings is used in place of the original.
To resolve this issue, copy the original user.config file from the original installation directory and paste it into the new sub-directory created by the Outlook update from Microsoft. After replacing the new user.config file with the original, user-specific file and re-launching Outlook, Auto-Import Folder Configuration should be restored.
In a ClickOnce deployment, where the Auto-Folder Configuration information is set in the deployment package and cannot be changed by users, you could also create an updated deployment package and redeploy the integration to the client machines.