When the html injection was disabled I could see the correct <head> section present in the pages being rendered with content="IE=edge" present. I noticed though that with injection enabled the Netscaler was injecting the script before the <head> on the page and I suspected that we were dropping the rendering level even before reading the head section.
To get around this I modified the prebody.js as below, adding another <head> section to the top of the page.
As an aside to get the logging working corrected I needed to modify my prebody.js to statically set my server name too. Not sure if I missed somthing else in config, thus needing to add the entry, or if there is some bug.
Below is a snip of the prebody:
Edgesight for Netscaler 2.1
Netscaler Version: NS10.1: Build 123.9.nc
NS10.1: Build 123.9.nc