A TiVo/V6 series link will always attempt to record the first available showing of any given programme. It sounds like you're setting the SL on what is (unbeknown to you) the second or third showing, and the box has probably scheduled the first available one.
The other option is that the SL is set to record "New only" episodes, and the programme in question isn't new, but a re-run. The first-aired-date will show this.
If you can post any specific examples, we/I can happily check.
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