Had a guy come in with a stock 5.3 4X4 truck, wanted DOD turned off. Not a problem, right?

After reflashing the truck, I go to crank it over and instead of firing right up it takes a half second before catching, and stumbles like it's running on four cylinders. This also happens on cold restarts, hot restarts are merely delayed.

1) Engine cranks for 0.4-0.7 seconds before turning on the injectors

2) I've only logged hot restarts, but typically the ECU commands ~4ms pulsewidth on both banks when it turns the injectors on. Sometimes it applies ~8ms on bank 2 for a moment - I ASSume that cold startups with more enrichment are doubling on bank two to cause the stumble.

I set the truck back to stock and it still starts up like this.

Any insight?