I would think you must be using very short lengths of thread to knot it at the eye of the needle like that. If I did this My thread would wear and break at the eye. I am constantly sliding my needle down the thread to avoid wearing a weak spot in the thread and have had it wear through enough to break when I forget to do it.
But I also take a much longer than average length. When quilting I cut darn close to a 36" length and I run it through bees wax to prevent knotting. When I start a new length of thread it is doubled over almost the entire distance. Every few stitches I slide the needle down it. I rarely ever get a tangle or knot. I like 30wt best for handquilting so the heavier thread may also help.
I have no knotting problems with silk thread when doing applique. Usually take about 26" cut of that.