After going back to registeronce and getting a new license file there does appear to have been something wrong with my original license file, dating from the time when the MayaS 2016 bundle was first released, as it was missing an "INCREMENT 86269SFTIMSIB_2016_0F" block. With this new license everything seems to work as expected.
Just never thought of having to update the license file,
as I wrongly figured the MayaS 2016 file would still be valid for the SP2 as well...