TM,
The spring clip on one of my chains did not seat to well in the grooves, but seeing as this has happened twice it can't just be the link.
Do you have a pic showing the alignment.
Simple trick i use is a piece of fishing line, hold it against the rear sprocket at the most rear point , then move it forward till it touches the other side of the rear sprocket ( see Pic) This works better than a straight edge as you can have the clutch on the engine and line up up with the smaller sprocket.