I've tried with the follow settings:
trill.setMode(Trill::RAW);
trill.setPrescaler(1);
trill.setScanSettings(1, 16);
#if DIFF_MODE
trill.updateBaseLine();
#endif
Somehow, I'm back to getting no readings... Also, I'm not noticing a very obvious difference in the readings when changing the prescaler.

This is how the readings look right now. Before I had readings that were noisy (giving me some values) but not flattened to 0 like the above screenshot.