The math, for your edification:
Xerath's W penetrates 40% of your opponent's MR, so you can say that they have 60% of their MR left
Enemy's MR: 60%
Now add on top of that the multiplicative stacking of Void Staff. Simply put, it reduces their MR by another 35% of 60%, so they lose another 21% of their total MR
Enemy's MR: 60-21 = 39% of original MR
subtract that from 100% and you get
100-39 = 61% MPen, or 61% of your opponent's MR that is not being used for damage calculation.
Not exactly 64%, but much closer to that than 75%... You might have also been running the %Mpen mastery, giving you another 8% MPen, which would calculate out to
8% x 61% = 4.88% of total MR penetrated. So it would be closer to 65.88% MPen.
I hope this was helpful, even if I still don't know how you got exactly 64% MPen.