I've never experienced slow moving bubbles, but I have done the same thing with the "bucket tilt." I have learned to prop one side of the bucket up with an object 1.5" to 2" in height before I start my auto-siphon. In helps a ton. I also started pulling the tube and the siphon ont of both fermentors as soon as I head the first gurgling. I just had a thought, the bubbles could have been because the elevation change was too little. I.E. The primary and the secondary were at too close of a height.
Hope that helps you out.