I'm not sure if you might be describing 2 different issues, but I can explain both.
The main thing is after you enable the Pen/Bezier or Pencil/Freehand tool and before you start drawing, look at the
control bar, which is the bar full of icons/buttons that is just above the top ruler. For the Mode, choose Regular Bezier Path (not Spiro Spline). Also, in the Shapes dropdown menu, choose None.
There is another issue, that has more to do with style (color, opacity, stroke width, etc.), than with path effects. It's completely a different thing that what you're describing....but still kind of similar. This article/tutorial will explain everything:
Customize Your Inkscape Tools' Styles. But feel free to ask questions, if you have any