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configure & troubleshoot anyconnect
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AnyConnect Client V2.5.1025 Installation Problem - Windows 7 Junctions

If you install the AnyConnect Client V2.5.1025 on a Windows 7 box which has a directory junction for the "ProgramData" folder (i.e the user has moved the ProgramData folder to a different partition and used a NTFS junction to redirect from the O/S partition), then the installation will delete the junction. This is easily spotted as the majority of the user's Start menu disappears.

Note that this scenario (moving the ProgramData away from the O/S partition) is increasing common with the advent of the use of SSD for the O/S partition.

The work around that worked for me was to immediately recreate the junction following installation of the VPN AnyConnect client.

Hope this saves someone some time & confusion...