OK - so - the act of re-opening them causes Roll20 to 'interpret' the HTML, turning them into their characters, and stuffing them up. This problem doesnt happen if you use the macro as abilities in a a character sheet, rather than a global macro, and there are other ways to get around the problem as well, but the funamental problem you are running into is as I described. Write your macro in a notepad text editor, and paste it in after every edit, and never open the macro ever unless you are ready to re-paste it in.
