Joel, while I couldn't find specific reference to it in the official IETF HLS spec, here's Apple's documentation on how backup streams are meant to be presented in the playlist files for use with iOS. It'd be helpful if Roku supported this as well, as I'm running across more and more providers that are using this standard.
Thanks for the fast reply Joel and TheEndless. The streams we are working with follow Apple's documentation. So it sounds like that is part of the issue we are experiencing. I'll post back when we figure out how we end up handling this issue.
I second the request for following Apple's documentation as we are also seeing lots of movement toward following Apple's implementation.