Just as a follow up to this issue if anyone sees this post. This turned out to be a Unity / Xbox One specific configuration issue. Due to some .meta file mix ups with our version control I was able to create a project where the XboxOne_Localization folder was created and configured correctly (containing splash images and logos) but the old method of assigning these splash images in the player settings was missing / corrupted.
I believe there must be a bug with XBO Unity building as you need both of these configurations set up and matching or the old image will flash on the screen. Corrupted, missing, default, or not, it will display!
I think any connection to NGUI is a red herring. Possibly the time it takes for NGUI to initialize itself is enough to make this issue visible on the screen. Sorry for the confusion!
Solution:
1. Delete or move Priconfig.xml from your project root directory.
2. In the player settings assign your splash image.
3. Move or recreate Priconfig.xml back into the root directory.
4. Build as normal!