Sorry to revive this thread.
Followed the instructions to update from 2.6.1e to 2.6.2
I updated once and it worked fine but had to revert back on SVN. When I reload the scene with 2.6.1e again everything is fine. Now when I update by creating a new scene, deleting the old NGUI (or overwriting the old), updating from the asset store and going back to the game scene all the Mono links are broken.
I have tried this process about 10 times now and the same result every time. Is there anything within the update process that can cause this to happen?
Johnty