Hi Khalid,
No much help really but I had a similar problem, long while back, where one axis only was gaining steps. These gained steps were produced from noise spikes which were treated by the controller as a genuine step pulse. Although they were random they were pretty consistent and my problem was finally solved by fitting another, better quality, breakout board which managed to filter out the extremely fast noise spikes.
Although it is unlikely to be the same problem I would suggest that you look for electrical noise as a cause of this event.
Tweakie.