The ConnectedMonitor and CustomEDID options apply to an entire GPU, so specifying different values for the different screens on a single GPU can lead to unexpected and confusing results. To make sure things work the way you want, you should probably specify the same things for both screens:
Option "ConnectedMonitor" "DFP-0, DFP-1"
Option "CustomEDID" "DFP-0: /etc/X11/MS_0025.bin; DFP-1: DFP-1:/etc/X11/acer.bin"
Also, UseDisplayDevice "DFP" doesn't make a whole lot of sense when both of your connected displays are DFPs. You should specify either DFP-0 or DFP-1 (or just remove the UseDisplayDevice option entirely).