Measure voltage difference between ground and DC floating power supply lines

Because the supply is floating, and you only made one measurement at once.

Floating means isolated, which means the resistance between the supply and ground is very very high. So high that the 10 Mohm input resistance of your multimeter is almost a short circuit in comparison.

^{simulate this circuit – Schematic created using CircuitLab}

If you were to make both measurements at once, with identical meters, you would find V- at -6V and V+ at +6V with respect to ground, and 12V of course between V- and V+.

Did you measure using DC on the multimeter? You need to measure the AC voltage that might be present between output and ground. Then you could see several tens rising to over one hundred volts AC - this of course doesn't mean it's dangerous - it's just the EMI decoupling capacitors (if any) on the output.

For DC measurements your meter's input impedance will likely reduce the voltage to near zero.