OK... it seems like the engine idle speed on your truck is too low. Idle speed with the transmission in Park or Neutral should be approx. 800 rpm (check your engine data label to verify). The idle speed on my truck when stopped and in gear, even with a low-stall torque convertor which really loads the engine, is approx. 750 rpm. When the ECM gets an "idle-on" signal from the APPS, the idle speed is controlled solely by the Fuel Pump Control Module (injection pump computer) and not by the ECM or APPS. In other words, the ECM tells the VP44 to "go to idle" and let's the VP44 do its job. I'm not sure if the VP44 normally uses any external references for controlling engine idle rpm.
You can verify the idle rpm isn't being influenced by anything outside the fuel injection pump by simply disconnecting the VP44 wiring harness then hot wiring it per instructions you can find here on the forum (do a search). Start the engine and if the idle speed is the same with the VP44 hot wired, then you know the problem must be internal to the VP44. If the idle speed increases significantly with the VP44 hot wired, then something external to it must be causing it to be lower when connected... like possibly a bad sensor.
If you are able to narrow down the problem as being internal to the VP44 and it's still under warranty, you may want to give Industrial Injection a call.
Please keep us posted,
John L.