The problem may be the throat. If it is all metal then during retraction the partly heated and rubbery filament and solidifies jams in the cold zone when it pushes down again. When you pull the filament out and reload it, you pull this jammed part out as well. This throat problem happens when in-filling as the print speeds (filament feed) are higher and heating/cooling dynamics change a bit.

To check this, if you go back to the ptfe tube throat and if the problem disappears then you know it is the throat which causes the problem. If so, then replace it with another brand all-metal throat. There are good electrolytically polished ones as well as high-lubricity ones in the market. Google is your friend.