Sounds like a poor ground. In this situation, the system will often work, but will confuse the diagnostics in the controller (be it integral or aftermarket).
If you get braking with the manual control, but not with the service pedal, it seems you don't have the system set properly (max voltage setting).
Also, why would you go on gravel to set the gain? This setup should be done on dry pavement (unless you regularly tow on gravel). Using the setup procedure on gravel will end up with the gain set too low (since it will be easier to lock the brakes), resulting in poor performance on dry pavement.
The goal is for the brakes to almost lock up (but not quite!) when you do a panic stop on dry pavement. To do this, any good proportional controller's setup will be something like:
1. Warm up the brakes on dry pavement.
2. Do a fast, full-manual apply from 25mph on dry pavement. If the tires do not chirp, turn up the voltage and try again, until you can lock them up.
3. Once you are able to chirp the tires, back it off just until it won't lock up anymore. Perfection!
thebrakeman ('70), DW ('71), DD ('99), DD ('01), DD ('05)
2004 Surveyor SV261T (UltraLite Bunkhouse Hybrid)
2006 Mercury Mountaineer V8 AWD Premier
Equal-i-zer WDH (10k), Prodigy Brake Controller