The shows were My Name Is Earl and Desperate Housewives. It did not check to see if it was deleted from my prioritizer, but I was able to change other shows just by deleting the MPEG4 show in the guide and setting up a new one.
If you just setup OTA it will take a day or so for the guide data to fully populate and index. It's possible that on some shows it doesn't have full guide data yet and so doesn't recognize that it's a series. I had this happen to me when I setup OTA for the first time. I waited until the following day and was able to setup series links as normal.
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