Sounds like there is some difference in the old and new cluster. You might be able to get it reprogrammed by the dealer, or it could be a hardware issue (best option then is to remove the low fuel lamp). ;-)
Well, that would point to an issue with the new cluster. What year is the new cluster?
If it’s used and is one from a 2004-2006 maybe the fuel gauge is defective, out of calibration, or bad connection at the connector/terminal. (The service manual has no info on recalibrating a fuel gauge).