I'm having the same issue.
The manual says pedals FS5-FS8 will only transmit if the POD is set to "Pedal Board" Mode. If this was the case then using a "Preset" to trigger a midi message for amp switching won't work. And this is exactly what I want to do too. And have been unable to.
Also the EDIT software doesn't save the midi settings when I change them and save the patch. I have to use the interface on the pedal to successfully change and store midi settings
If there IS a way to send a midi message on the transition to a Patch, when in Patch Mode, please let me know. I'm sending from an POD HD500X to a Voodoo Labs Controller-Switcher, THX