As the title states. I believe it has to do with the shared hotbar default settings. The PS4 automatically loads with its own default settings, like anything found in the character configuration menu, which are not part of the settings which are transferred over. Since I made changes to the shared hotbar settings on the PS3, that data will not transfer over and are now left with messed up hotbars and having to redo the ones that are messed up all over again. If anyone does have a fix for this, I would love to know.

P.S. I loaded up the PS4 and made the changes to the shared hotbar settings exactly like I have on the PS3 and saved it. Then attempted another transfer, but all it did was revert back to the same PS4 default settings.