It should not affect the way the phone worka or loads in any way. I had this happen to me a few days ago and posted in one of the help threads my process to remove it. As the above post states though it has something to do with one or more specific things that are part of the rom you are flashing. There is actually a post in here called "can someone try this" or something to that effect detailing a soft fix that seems pretty easy. Do a little searching in the at&t sgs4 forums and you should come up with a few things.
Sent from my SAMSUNG-SGH-I337 using xda app-developers app
Samsung Galaxy s4 on MF3 firmware, rooted and safestrapped running...
-Deadly Venom v8.1
-ViSiON X MF3 Blue Ice
-Intika Locky MF3 v1.0
Samsung Galaxy tab 2 7.0" rooted running Slimbean w/ android 4.2.2