Couple things to remember when using your rotary cutter...does not cost anything... You cut only as far as your outstretched hand can reach & if using a thin (6" or less wide), put your pinkie off the opposite side from where you are cutting...this will stabilize the ruler.
One other tip I've found useful when cutting 4 layers or less... get a thin piece of quilter's tape (I use painters tape I've trimmed down...straight edge to the inside of the ruler) and put it along the 1/4" line on the ruler where it will be on the bottom/underside of the ruler, near the opposite/outer edge of the ruler...you can butt this up to the edge of the fabric and it will also help keep the cuts straight.
One thing that may be happening, and have nothing to do with your cutting...drifting when sewing...measure your stitched seams...do they seem to get a couple threads smaller as you get to the end of the piece you are stitching. If you notice that you are drifting...mark the very end of the pieces 1/4" in ...just a dot...it will let you know if you are drifting at all.