Kia Troubleshooting Questions? Ask a Mechanic
Welcome, I'm Chris (aka Moose) I prefer working afternoon till just after midnight.
From what I gather from your description all power door locks now work form the switches and fobs but the liftgate works opposite from its command. If I understood wrong, let me know. SO far this looks like a smart key control module failure. Do you have a diagnostic tool and do you understand wire diagrams?
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Left side of the dash, does your model have serviceable lock and unlock relays, if so then we have some electrical testing to do there from this diagram. https://dl.dropboxusercontent.com/u/90220402/soullock.pdf
I do not have another diagram that shows where that junction block is. I will opt out and see if another has it and can help from here on out. Best of luck.