You can try to configure your VPN without the Fortinet GUI. Here's a complete guide to IPSEC for linux http://www.ipsec-howto.org/ and you may want to try this:
The link is created by running pppd through a pseudo terminal that is created by pty-redir and connected to ssh. This is done with something similar to the following sequence of commands:
/usr/sbin/pty-redir /usr/bin/ssh -t -e none -o 'Batchmode yes' -c blowfish -i /root/.ssh/identity.vpn -l joe > /tmp/vpn-device
/usr/sbin/pppd `cat /tmp/vpn-device`
/sbin/route add -net 172.16.0.0 gw vpn-internal.mycompany.com netmask 255.240.0.0
/sbin/route add -net 192.168.0.0 gw vpn-internal.mycompany.com netmask 255.255.0.0
What this does is run ssh, redirecting the input and output to pppd.
The options passed to ssh configure it to run without escape
characters (-e), using the blowfish crypto algorithm (-c), using the
identity file specified (-i), in terminal mode (-t), with the options
'Batchmode yes' (-o). The sleep commands are used to space out the
executions of the commands so that each can complete their startup
before the next is run.
From "Bring up the link"
Next section, "Scripting" may help you as well to configure and run your VPN client. There's additional information in the ubuntu documentation.