I can not think why a rotation transformation would affect quality unless you were doing an axisymmetric model and moved it into negative R orientation. Is there not some element number given for the bad element and you can then show the before and after transform shapes to understand the change? Maybe it is property related or MPC related?
Like I said the model without rotation works. Also the model with 45 degrees rotation works, but the model with 90 degrees and -90 degrees rotation are not working.