The IOref is tied already on the MKR2UNO to 3.3 as it should be.
If you change that there is a possibility of damage to the MKR.
Some shields may need LEVEL SHIFTING to operate correctly with IORef.
I wonder if this is what is happening in your case.
You would have to examine your shield to see if that is the case.
Without a schematic of your particular shield I would be just guessing.
There are so many motor shields out there each may need a slightly different approach.
Also still bear in mind the different MCU architecture too as that could be quite important in the way timers and PWM are used especially. (sketch required)