The log I posted in my original post comes from a cook in which we deleted Intermediate and Saved folders.
You have also all the options we are using on the command line above, we have tried different configurations in regards to cooking and all result the same.
Here are our packaging setting again in case:
-clientconfig=Development -serverconfig=Development -nocompile -nocompileeditor -installed -utf8output -platform=Win64 -targetplatform=Win64 -build -cook -map=…ListOfCookedMaps… -unversionedcookedcontent -pak -createreleaseversion=testing -manifests -compressed -stage -package -cmdline= -Messaging -CrashReporter -unattended -clean
We think the problem is in how we set up a particular asset in code, a collegue described this well, I will post in as a reply to this: