Besides trying it with a really nice flat reference to determine the error (like MDF, which just typing sends me into sneezing fits...), try this:
- Keep the fence up and locked when adjusting the fence height.
- After locking the height adjustment, you can tilt down the fence and lock it.
Mine (which is a first-gen pin-style Domino) will have slightly tilted mortises if I adjust the height with the fence not locked upright.