The profiling software should ignore color patches that have a higher total
ink build than what is called for in the total ink user input field so it
shouldn't matter how much higher the RIP total ink limit is set. Right?
Well the profiling app is telling you have too much ink which is why it's
building it at much less than your RIP ink limit. You may look at reducing
your ink limit at the RIP and you might find the shadow reversals (too much
ink) go away. 360% is a lot of ink on paper so you must either A) have a
super coated stock and/or B) not using a high printer resolution which would
put down twice as much ink.
I determine the sweet spot for RIP ink limit by evaluating different ink
limit settings in ColorShop X. Look for the darkest L* and that's where you
should set your ink limit. Use the same ink limit setting in reducing your
profiling chart ink coverage.