Hey,
The step sequencer of the keystep is polyphonic, while the model D is monophonic. What happens is probably that you play 2 of the notes legato, and the sequencer registers it as 2 notes for 1 step.
To make sure you have the expected number of step, you have to make sure to release your finger after each note you want to enter. I I I found out that using only one finger to record the notes can help.
Hope this helps,
Victor