I am having a similar issue, but not sure, from the wording of your question.
I also use Pro Tools. The basic automation works on all faders, but faders 9-16 will are not controlled by the automation buttons (Trim, Latch, Write, etc.), and also will not work in Send mode. The last 8 faders stay At the position they were at, for the volume, and have no effect while in Send mode. (The first 8 faders snap to the bottom - if there in no Send level being used - as they should.) I have had a Faderport 8, since the week they came out, but just recently switched to the Faderport 16. I’m not sure, but I think this only started happening after installing the new firmware from the end of March (2019). Maybe there is some bug that prevents some of the functions from working on the last 8 channels of the controller.
Update: All is working well in Firmware v3.32 and v3.42.