I have been more of a shadow on these forums but thought I may be able to add something to this issue.
It sounds like your rig is factory setup with dual alternators. Most up fitting has dedicated auxiliary power outputs as mentioned by someone else in the thread.
Where is you power feed for the DC to DC connected?
My thought is that the chassis/pcm/BCM monitors the starting battery with the shunt and current limits the charging based on what it expected for the starting battery. By adding your output cable between shunt and starting batteries the chassis thinks it's charging to much and limits current.
Most vehicles especially Fords have an aux power location. Usually they are in a fuse block or terminal block somewhere on the vehicle. Many times they have fuses, relays and dash switches depending on your models package.
Ford should be able to tell you what options you have and a wiring diagram detail where there located. Owners manual usually also outlined the locations and current the circuits are designed for.
If the chassis is as "smart" as I suspect it may be the only way. You may have to connect each dc to DC to a separate circuit to get enough output current.
Good luck, cheers