I should mention I'm on SailFish 7.6 using Simplify3D (latest 2.1 version). I have tried un-installing Simplify3D and re-installing.
Anyone have any suggestions or has seen something similar?
From this I think there a couple possibilities:
1. The g-code for the print is just wrong.
2. The firmware for the printer is corrupted.
I'm fairly confident by replacing the mounting screws with nylon screws (and using nylon washers between the boards and the standoffs) on the LCD board and SD/buttons board I have resolved the original problem. I have done several 2-3 hour prints and it would have failed many times before doing the same prints. So hopefully if others see this they can try this fairly easy and cheap method to fix the issue.