I'm seeing odd behavior, or it could be by design. I have a set up for users on a particular side of the network to access the ssl vpn to provide additional resources on the network across an mpls ciruit (not a typical vpn session from an external public network).
I have it working perfectly, but when the session is established, it turns off the proxy server settings in IE and it adds the automatic config script for file://C:\Users\userid\AppData\Roaming\Juniper Networks\Network Connect 8.0\instantproxy.pac.
I need to have the proxy server remained enabled after an SSL VPN session so the user doesn't have to keep manually re-enabling it after every vpn session initialized.
instantproxy.pac is created if you have a proxy configured via the vpn tunneling connection profile. You can configure it to no proxy server to avoid this issue.