In /etc/skel/.profile the $HOME/.bashrc file is sourced before PATH is
fully configured with the addition of $HOME/bin.  Please set up PATH
fully before sourcing the .bashrc file.  Otherwise upon initial login
processes from the bashrc file has one PATH (without $HOME/bin) but
other instances have a different PATH (with $HOME/bin).

To be clear, please put this part:

  if [ -d "$HOME/bin" ] ; then
      PATH="$HOME/bin:$PATH"
  fi

Before this part:

  if [ -n "$BASH_VERSION" ]; then
      if [ -f "$HOME/.bashrc" ]; then
          . "$HOME/.bashrc"
      fi
  fi

Presently it is the other way around.

Thanks,
Bob