I am using rtMedia with Buddypress and Woocommerce. When I Regenerate my Thumbnails (with Regen Thumbnails) I lose all of my sizes except for the rtMedia sizes. If I deactivate the rtMedia plugin and regenerate, I get all my sizes updated.
It may be a conflict with my theme or another plugin but, for now I can work around this issue. I just wanted to bring it to your attention.