It sounds like you may have an idea about what went wrong, but let’s go through it. Pressure transmitter 🙂
Differential transmitters use the laws of hydrostatic pressure to calculate the level in a tank. I’ll bet that when you set up your devices, you forgot to factor in the change in density of your fluids with the decrease of the temperature in the tanks. Chemicals like ethanol have density changes of around 20 percent with changes of 20 degrees Celsius.
I suggest you use a probe level measurement like one from Endress+Hauser that can measure both the level and the temperature profile in the tank. You may also want to consider switching to a different measurement method more suitable for your configuration.
One of these companies may have a tank gauging solution for you: