Twan-
Is your turbo a stock turbo? W/226k mi? Stock trans, tires etc etc?
I'm just curious if there isn't an underlying issue...
The turbo brake that came with the tuning I had was not only noticeable, it was darn right attention grabbing if you were running some RPM! Also, switching from 3-4, or 3-5 should be a hoot, the power is absolutely noticeable. My tuning was for a built trans but the 3-4 gain for me should've been similar as your 3-5, but the tow tunes should be nearly identical for a stock trans stock engine truck, mines an LBZ.
You mentioned raising 8psi with the turbo brake, I remember more like 12 or more, and actually IIRC I remember seeing up to 20psi a time or two with the stock turbo but that could just be my bad memory. I know it was more than 8psi tho.
Maybe you're vane sensor is going bad, maybe the vanes are clogged with soot?
Also, are you positive the switch is hooked up right? Good connections? Are you sure the switch is good? Maybe only the odd positions are functioning, it's happened before. Each position sends a certain low level voltage. I don't remember what they are but you can test the switch.
And you're absolutely sure the right files loaded?
I know with my tuner, if the switch is hooked up wrong and you successfully load the tuning, the default tune is the max effort tune, and you can't switch from it. I'm not sure if ATP sets theirs up like that of not.
Although if indeed you're getting "some" turbo brake action, and you're noticing power differences between switch positions your switch is probably hooked up properly.
I'd let them know you're not satisfied, this is supposed to be a simple task, easy and painless, if they're sending out tuning for a stock truck it's a generic file that they've created and they basically cut and paste it into an Auto-Cal set up with your VIN, or they send you an auto cal and you load the tune. They send the same basic file to everyone who owns that year truck with the similar/same options. It's nothing "special"...
So I'm wondering WHY they would need "data logging" unless they're trying to trouble shoot an underlying problem for you, but if so, really they should be saying that upfront as they should know exactly what tune got sent to you...