If I'm reading the schematic correctly, you are using Q1 and Q2 to connect your GND to the Chassis-GND.
Is that your only connection between the two? Because if R12 is connected to the chassis, and the ENABLE-Pin is LOW (i.e. GND), then the 1.4V is the difference between GND and Chassis-GND.
Meaning, all your LOW-Signals are 1.4V, relative to the chassis.
Does that make any kind of sense? I sure hope so, I'm a bit tired, sorry :-)