Hi pcdwarf
I cannot reproduce this on myself (5.1.9), or I did not understand the problem.
For a simple test I created a device with two visible power pins, GND and VCC (Picture 1).
This device is used twice in the circuit.
GND is connected together and the VCC pins are supplied with different voltages (Picture 2).
When generating the PCB, both voltages are cleanly separated (Picture 3).
Greetings
Hubert