I had a custom mail handler, based on "Create a new issue or add a comment to an existing issue", that correctly stripped the reply/forwarded text from gmail responses and added the incoming comment to the JIRA ticket. However, it did not strip the reply/forwarded text from Outlook email, which is the majority of our email.
I used Chris Marts' regex statement in an "Add a comment before a specified marker or separator in the email body" handler and now have the Outlook responses working perfectly. Thanks for sharing, Chris. Unfortunately, I have totally lost all gmail comments. I receive an email from JIRA with the comment, but the comment is not added to the ticket.
It seems that the 'create new or add a comment' handler can strip quotes but not split regex while the "add a comment" handler can split regex but not strip quotes. At least that is what I see in the UI. Don't suppose there is a file in the bowels of the directory structure that could be edited to do both? Assuming that this is my problem. 
Any assistance on this would be deeply appreciated.
Sally