Only have that problem on the Janome 8900 with the narrow 1/4" foot - just as others have mentioned, once I put the larger/wider foot on, to fully cover the wider feed dogs, the problem is gone! I also am consistent in using a 'seam guide' to the right of the presser foot to ensure I line the fabric up correctly - without it I find my stitching gets a little wavy.
Curious what machine you have?
Christine