Hi Adam
I should think it’s due to the bottom layer having extra time under the heat, I have had this problem on single layers when using recommended time (as in a previous post). Problem was resolved by reducing time down to 10 seconds, 130 deg C heat and VERY light pressure-I just hold the press down now instead of clamping, peel after a few seconds, then put back under for 10 secs full pressure.
I’d suggest experimenting with how little time you can get away with on both layers, then give a full press when done.
( I also use Grafiflex )