Apologies, I wasn't clear. I meant to say that you'd want the transparent setting to be *disabled* (not enabled). If it's already disabled, then leave it as is.
Having thought about this more, I don't think there is a way to stop this behaviour due to the full proxy architecture of a standard virtual server. When F5(1) connects to the F5(2) virtual server, F5(2) will subsequently send SYN Packets to the back-end pool member.
With regards to AFM, you can create a tcp-syn-flood DoS profile and apply it to a virtual server, but I believe you can only rate limit on a per second basis (e.g. 1000 SYN packets per second or 100 SYN packets per second per client source IP).