As I used to hear said when I was much younger, "well I'll be a monkeys uncle". I actually heard back from Rovi, here is the response they sent.
"The issue regarding OTA channels not surfacing to the WMC guide is believed to be resolved and they should be visible in 24-48 hours. Please run through your WMC setup (if necessary) to confirm if you now have the missing channels along with their corresponding guide data.
If you continue to have issues please open a ticket with Microsoft in the Connect application (
https://connect.microsoft.com/site1145/Feedback). Microsoft will work directly with Rovi on any further issues you might be having.
Thank you,
Rovi Support"