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2007 Yukon Denali won't retract

My wife’s 2007 Denali is having problems with the retractable running boards. When she had the car for a year the battery would misteriously disharge for no apparent reason. When she took it to the Dealer they told her that it was the program for how quickly they were supposed to retract after you closed the door. They re-programmed the module and it worked fine for a year. Last week we just completed a 5.5hr. drive and were unloading the truck. The engine was off for about 1 hour and the doors and headlights were on. When we went to restart it it wouldn’t start. The truck jump started just fine but when the engine started the Check Engine light illuminated and stayed on and the running boards would not retract. I recharged the battery (let the engine run for 30 minutes) and it started fine but still no running board retraction. The next morning we went to start the truck and it continued to start fine however the Check Engine lite went out but the running boards stayed out. that was 2.5 weeks ago, the truck continues to start, still no check engine lite, still no running board retraction. Does anyone have any ideas what is going on?

Sounds like you have to have them reprogrammed again. They must have lost memory after losing your battery’s power.