Well, even after the Win8.1-Update 1, still the built in Junos Pulse does not work. Even on Windows 8.1. You still have to install the desktop version for VPN access. Why have the built in versions, if you can't use them?
Junos Pulse has worked for me on my RT since the original 8.1 update. It also works on my home desktop computer. The built-in client is much better than the client/process on Win7 and earlier. I'm wondering if your employer's Juniper VPN configuration is the problem.
When I originally was setting up the built-in client, I made the mistake of including extra 'stuff' in the 'Add a VPN connection' dialog which caused failures. For the Server name, do not include 'https://'. Just put in the address of your VPN server. (e.g. 'vpn.youremployer.com')
Save.
When you invoke the VPN session, it will prompt for your username and password. Use the exact credentials that you use on your VPN web portal. I originally made the mistake of adding my domain. (e.g. domain\username) This failed, but again it does work using the exact credentials used to authenticate to my employer's vpn web portal.
I imagine you've done all of this, so I'm assuming it has something to do with how your employer has deployed the server. Good luck!