Hi,
Not sure if there is an easy answer. I would suggest just entering the prompts yourself, rather than having SAS search your code to guess at what might be prompts (which is what I think of from the 'prompt from SAS code' button). It's not surprising to me that global macro variables that are commented out might still be seen by the 'prompt generator' routine, because it might not know enough about the SAS language to recognize all the different kinds of comments. I think it's easier just to make a list for yourself (perhaps in a header comment block), defining all the prompts your code expects, and then use that list to create the prompts.
HTH,
--Q.