Brian,
First, you need to tell people that the file you have included is a library (.llb file), because when I download it, it doesn't have an extension.
Next, I see where you have start the master board analog input acquisition, but I *don't* see where you have started the slave boards. You configure them, but you never start them, so they're not waiting for the trigger from the master.
I also don't see where you start your counters, either...they are configured (programmed), but never started.
Mark