Yesterday, I had an h264 render without the LUT I had applied in Cortex. All other files of both delivery types (Avid DNxHD and h264) rendered with the LUT applied.
I re-rendered the one file with the issue today and it rendered properly.
When this happens again, please export the logs from Cortex with the problem job open before re-rendering the clip. Send these logs to support@mtifilm.com.