I just finished setting up some Z-up templates. I don't want users to have the option of choosing Y-up, I want everybody to be using the same system. However, after creating the new template, and then pointing to it in the Default Templates location, for some reason it messes the template up, and no matter whether you choose Y-up or Z-up, the template does not come in in the correct orientation.

Steps to recreate:

1. create a blank new file.
2. apply Z-up view
3. save and close template
4. TEST STEP: re-open the template. it should open in the same orientation as it was saved.
5. set the Default Location in settings to the new template
6. create a new file using the template. The option for Y-up or Z-up is now no longer greyed out, and regardless of which option you choose, the part will flip 180 or 90 degrees immediately. 
7. change the Default Location back to a different template
8. create a new file using the template. It opens correctly again.