I had to install potrace to get PNG to SVG to work at all. Similar issues to what you describe.
From PNG to PNG, this works for a single icon:
convert ~/.local/share/icons.new/icon.png -alpha set -fill "#FFC107" -tint 100 -density 600 -format png ~/.local/share/icons/icon.png
You might have to do a 'find' or something and write a little script for all in a set of subdirectories.
Do you need SVG as the output? I think this will work for SVGs as the input with some trivial changes.