I know that this is an old thread. But we are experiencing the same problem.
It happens not only when making iOS builds with override checkbox ticked, but also when reloading the scene after reducing Max Size in the Default tab of atlases. Note that it only happens when the size is made small enough.
It seems to us that NGUI doesn't pick up such changes made to atlases. Or to be more specific, the UVs of sprites are not updated when such changes are made.
Could you please have a look at the problem, ArenMook?
Not sure if this is related, but here are our settings in the UIRoot:
Scaling Style: FixedSize
Manual Height: 2048
Shrink Portrait UI: Unticked
Adjust by DPI: Unticked
Cheers,