We're currently in the process of looking to upgrade the Junos Pulse client on all our machines due to the Heartbleed vulnerability. We manage and install Pulse using SCCM and have client updates disabled at the gateways as we want SCCM to manage the desktop.
We're going from client version 4.0r7.0-b41347 to 5.0r3.1-b44983 and are installing using the command line with the correct msi inserted where required:
msiexec /i j-pulse-win-4.0r7.0-b41347-64bitinstaller.msi CONFIGFILE=C:\Temp\PulseSettings.jnprpreconfig ADDLOCAL=PulseSA,SAEndpointDefense,SAHostChecker /qb
However we get the attached message displayed when upgrading the client.