I had the same problem initially; no matter how much I denied it, I was (subconciously?) peering over the nose. Your desire to 'see the numbers' is holding you back. You will find, I think, that your daylight landings are so blighted but less obviously.
Have your instructor turn off the landing light at short final (reinstating them when securely on the ground!) and conciously look at the far end of the runway. Watch the vanishing point and those perspective lines rise just like they do in the Thom manual.
This will improve your daylight landings as well. It's just a phase, I found...