Do you have rules allowing traffic in both directions? You need to have
firewall rules that allow traffic from Cisco side to Fortigate side, and
then from Fortigate side to Cisco side. Also, ensure NAT is disabled in
your rules.
I believe Phil is correct. This is exactly what I had to do. I was also
going to suggest this, however I wanted to see a diagram of your
topology first.
Can you post a simple diagram of your topology? I was having a similar
issue and I may be able to help, but I need to see what your topology
looks like. From your description, I think I am missing a piece of the
topology. A diagram would be helpful.