Full Resolution Femur sample:
Run the registration Using URAL, default parameters, Subsample=8,with Finetune=1.
Timings:
Primitive generation:   3 min
AutoFocus:                  50 sec
FineTune:                     25 sec

Result is below.  I don't see a need to change anything about the registration FineTune.
MI problem has to be investigated.