First, the setup: I've got a new TiVo Roamio, a TiVo Premiere and a TiVo HD. I quit cable a few months ago and am exclusively OTA now. I have all my shows stashed on my Roamio right now.
The Issue: When I browse the shows on my Roamio from my Premiere, a significant smattering of them are all flagged copy protected. This seems to have only effected shows recorded by the Roamio, not shows that were transferred to it from the HD or Premiere. Additionally, the arrangement seems random, even random episodes from the same show are flagged while others are not. What makes this especially odd is that none of these shows are showing copy protection flags when I browse from my TiVo HD or from my PC using kmttg, they only show as copy protected when viewed from my Premiere.
I did a full "Clear and Delete Everything" on the Premiere and the exact same shows/episodes are still showing the copy protect flags on that TiVo.