Could you give a more detailed use case what you have? What is the command you are using to include images?
HTML signature files can attached using --html option that creates Rich Text email body. Using --attach option adds images to mail and you don't need to use --html option when using that.
For example, following command sends mail with HTML signature and attached images.
CLENotes --password=password send --firstname.lastname@example.org=testing --body="html sig" --file-signature=signature.html --attach=adobe.jpg --html
By the way, inline image probably don't work.