I know this thread is old, but it must exist.
I got Juniper VPN working on Mint 13 i386. The issue isn't with MATE, it's a series of issues with Java, Mint, and Juniper's client.
Step one may not be necessary. I've been in the habit of removing OpenJDK as soon as possible, and replacing it with sun-java in order to get Juniper VPN working. Subsequently, I didn't even bother to wonder if OpenJDK is finally to the point where it works with the Juniper client.
1. Purge OpenJDK, install Oracle Java. Through the package manager is the best way as usual. Follow the instructions here
http://www.ubuntugeek.com/how-to-install-oracle-java-7-in-ubuntu-12-04.html.
2. Add xterm. It's not installed by default and Network Connect requires it.
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user@host ~ $ sudo apt-get install xterm
3. Under FireFox, you'll probably notice that once you authenticate, the Network Connect viewer appears and then just vanishes for no reason. I couldn't find any errors in the Network Connect logs, but I did notice that the ncsvc.log just kinda stopped right around where it was setting DNS servers. Mint 13 doesn't have /etc/resolv.conf. In order to fix, simply:
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user@host ~ $ sudo touch /etc/resolv.conf
You should be able to use the client now without any issues.
The downside is that adding resolv.conf is
not the Ubuntu Way™, so at best this can be considered a workaround. It seems to work fine on my system so far, and nothing seems to be broken. If you find yourself experiencing DNS issues during a VPN session or after a VPN session, check there first.