It isn't an altitude thing because the truck will take that into effect. There is a sensor in the drivers compartment, under the dash for this purpose.
Remove the tuner from the truck to see if that is the source of the problem. You should always start at the tuner.
Next, it sounds to me as though you have a FICM issue. This problem, if ignored, can result in damaging the electrical side of your injectors.
The FICM is an aluminum box that is on the drivers side valve cover. On the top of that box, you will see a small cover that is held on by a few torx style screws. This cover will need to be removed to test the FICM.
BUT, before we get too far into this, the first thing that should be done is to remove both of your batteries from the truck. Run them down to the local auto parts store and have them load tested. Load testing is free. Should either of the batteries test as marginal or fails, replace BOTH batteries. Proper voltage being supplied to the electrical system is VERY important at start-up.
Next, once you get the batteries home, put them on a battery charger. Even if they are new. You want 100% charge in them.
Before dropping the newly charged batteries into the truck, check/clean the connectors and check the cables. You might even want to give the connectors a coat of that anti-corrosion spray. Install the batteries, get out your multi-meter, THEN remove that cover.
The following link will tell you how to check the FICM at the three critical points in time. Once with key-on, engine off....once while cranking the engine over....and lastly while the engine is running.
LINK TO FICM CHECK