FACT: If you are allowed to submit opening pages along with your email query pitch letter, including the prologue pages will kill your query 99.9% of the time and agents won’t ask for sample pages.
Kristin goes on to explain why, but it’s basically because the tone tends to be so much different to the rest of the novel. If you’re querying an MS with a prologue, best to leave it off and start with your actual Chapter 1 for your sample pages.
That being said, I submitted Liesmith‘s prologue to Sara–who worked for Kristin at the time–and she forgave me for my sins. So… yeah. There are no rules, only guidelines, and all that.