I have same prob. I've got an aftermarket high output alternator, SCT shows 13.5V steady. If your windows don't work when this happens it's a problem with your cluster. The battery keep alive circuit or whatever and probably has a broken/cracked solder contact. I'm positive that's the problem with mine because I also can't "save" a time change after I turn the truck off. My clock on the radio is an hour behind... I took mine apart a while back and couldn't see anything wrong even with super close inspection- naked eye no magnification (which is truly needed, I am an aviation electrician), so I put it back together and it worked for a month daily driving no issues, then came back to doing it everyday.
I'm waiting until next time I take two weeks off work to tackle it again and send it off to circuitboardmedics. They have an advertised 1 week turnaround. They seem like good dudes and helped me trouble shoot a speedo issue on a 7.3l over the phone for free.