I’ve seen similar with a standard schedule. Did you try recreating the publication from scratch, ensuring that the reports are purged including prompt values and setting the prompts when scheduling the publication, not whilst creating the publication…if that makes sense?!
I tried recreating the publication from scratch (then adding reports, etc.)… Even in this case, I can’t change the prompt values. (It stays with the values the reports were saved on)
Changing prompt values on publication seems like a normal practice.