Alternate Part variant keeps updating PCB

[DutchGert]

Hey guys,

I have a weird problem that I don't understand when using Alternate Part variants in Altium 16.

I have an FPGA design where I want to use variants to choose between different variants of the same pin-compatible part (Zynq Z-7010 and Z-7020 in CLG400 package).

The only difference between the parts is one of the banks of the FPGA that is N.C. in the Z-7010 part and has usable I/O in the Z-7020 part. PCB wise the parts use exactly the same footprint.

What happens is that when I select the alternative part, Altium correctly switches between the two selected components when I select the corresponding variant. However, each time I update the PCB from the schematic  it reconnects a lot of the pins of the part... Afterwards everything is still the same and connected correctly (as expected) but it keeps finding changes and updating the PCB each time I  "Import changes from ..."

Does anyone have an idea what is going on here and how to solve it? Thx