Difference between Y-axis with Performance Kit

I have a strange phenomenon where there is a difference of ~6.3 mm in travel distance between the two Y-axis. Here are some details:
- Machine: Stepcraft-2/D.840 upgraded with the Performance Kit.
- Replicate problem: 1. Home, 2. Jog all the way down the Y-axis (~836 mm), 3. Measure the distance between the front panel and gantry.
- In spite of the difference there is no emergency stop, as should be when the Y-axis gets out of sync.
- If the Y-axis does get out of sync there is an emergency stop, so the sensors are working properly.
- When untightening the rollers or adding more grease on the lagging side, it makes no difference.

When doing some calculations, I found the following:
- The gantry moves 0.0075 mm per step.
- The travel distance is 836 mm.
- 0.0075 x 836 = 6.27
- Could it be so that one of the steppers is losing one step per millimetre?
- If so, could it be a firmware problem or a stepper problem?

Any suggestions on the cause of the phenomenon would be much appreciated.