I have xfinity configured with custom DNS and used to have a somewhat similar problem. At the same time each day, DNS would stop working (but I could still reach plain IPs) for a couple minutes.

It went away after I called them and had them "de-provision" and "re-provision" my modem. Basically deleting it from their system and readding it. For whatever reason, whenever I'm having chronic comcast weirdness, having them do this solves it. It sucks that this is the way things are.