Thanks for your efforts to help, while troubleshooting this I have turned to like the messed up terrain more over the “correct” one and have decided to simply not bother anymore.
I still wonder why this occurs and I agree with you SCDS_reyalP that I believe it is a file/order order issue in the pk3’s.
I have not shared the file (part from with Loffy whom I know) as this (without pointing fingers) have in the past proven to be a good way of getting the map out prior to release.
I would share anything with him besides my girl, my computer and my beer 
