Are you still working this issue?
If so, this might help. As always, save a backup of your config before making any changes.
Adding these lines to my config.boot file and re-importing, allowed me to establish a site-to-site VPN while using a DDNS service for one side. To use a DDNS service for both sides, add both lines to both sides keeping local and remote hostnames according to the pattern.
Static IP side
site-to-site {
peer xxxxx.hopto.org { (Enter the hostname for the remote DDNS. Already there if you used the GUI)
authentication {
mode pre-shared-secret
pre-shared-secret xxxxxxx
remote-id @xxxxx.hopto.org (Add this line here for the remote DDNS hostname)
}
DDNS side
site-to-site {
peer xxx.xxx.xxx.xxx { (Enter the Static IP Address for the remote side. Already there if you used the GUI)
authentication {
id @xxxxx.hopto.org (Add this line here. This is the DDNS hostname used for the local side)
mode pre-shared-secret
pre-shared-secret xxxxxxxx
}