I am having this issue as well.
At&t s4 4.2.2 mf3 1337 ....except mine has been rooted. I've had the phone for not even a month. I haven't done much to the phone, only rooted for a few basic operations. Has been running smooth up-until today, today it shut down twice randomly with plenty of battery power. It doesn't restart, I have to manually turn the phone on. The first time I wasn't able to turn my phone back on for a few minutes, odd. And the second time was around 10 minutes ago, it just randomly shut off. After holding the power button to turn the s4 on the stock boot up screen appears. Holy crud, it literally just happened again as I was typing this. This time its on the charger.....Sigh quite annoying. But yeah, the stock boot screen appears instead of the rooted "Samsung Custom" screen with the unlocked padlock image. Once I get to the password I get an "updated" blip that appears (updated time and date, I believe), yet I see no other changes to my phone. I ran rootchecker and it says I'm still rooted and I'm on the same firmware/ect, no update.
Some other threads I've read mention the exact same problem I'm experiencing 98% of them haven't been rooted and they are fairly new phones (months old). A few peeps posted that it was a battery problem and to check to see if its expanding/bulging, which mine isn't. These other threads haven't confirmed a solution, I was curious if anyone in this thread has found an answer to this highly annoying/recent problem?
Thanks.