Battery tested good, but engine code is "system voltage low."

I have a 2016 Jeep Wrangler. It has been very cold here between -1 & 20 degrees. The battery sat in the vehicle completely dead for about 5 days. In the cold weather and snow. Today I jumped the battery off with my truck. Got in the jeep and drove about an hour n a half & the check engine light came on flashing and dinging. The jeep started driving a little rough. I stopped at AutoZone and had them check the battery, alternator, & starter. All tested perfect. The code that he was getting from the engine was "system voltage low." He reset the codes. Now the jeep is still driving a little rough, and the engine light comes on flashes, dings, then goes off completely. Then about 5 minutes later it does it again.