When converting projects from RH 8 to RH 9 (HTML):
A pair of boxes replaces punctuation; usually when the punctuation is some mark (such as a comma) followed by an end quotation mark [see screenshot below; should be "A." not what is seen instead]. Boxes do not appear while working in RH or when viewing a topic from RH. Only seen when the project has been generated.
This suggests that your encoding is off. Do you see this behaviour when published to a web server or also when you are viewing your output locally?
In your SSL recipe, check the encoding you selected. Try setting it to default encoding or UTF-8.