Is this show currently broadcasting new episodes, or are you trying to catch it in syndication/rerun? If you only want new episodes, change your timer to new episodes only. That will trigger the DVR to record only the episodes aired with the tag NEW or with no tag as to the original air date. You may still get duplicates if reruns are tagged NEW or untagged at all, but duplicates should diminish.
My Hopper was doing this too. (before it crashed this morning) It was as if it didn't recognize the previously recorded SAME Episode as the SAME episode. Around that same time this problem developed ( around Jan 1st) I had recordings Fail. I know it recorded. I had already watched the recording, but when I attempted to watch it again, I would select Start Over, I would see about a second of black screen, then the end of recording DELETE/ DVR/ Live TV menu would pop up. I have no answers for you.