06 5.4 engine trouble when using tunes

[King_Ranch_Pilot]

Hey guys,
I have had my gryphon tuner in my 06 f150 5.4 3V for about three months now. The problem is, when I set one of the custom tunes in the computer, the engine runs good for about a day to two days and out of no where I'll be driving and it starts running extremely rough. It almost sounds like its missing some cylinders and this happens while I'm driving. When this happens, I pull over and return it back to the stock tune. After that it runs fine. What is going on and what can I do to fix this problem? It is very annoying. Thanks for your help.