This seems off-the-wall, but one of the research assistants in our plant science department asked how old your primers were. She had a few sets that would stop working after a month or two--even if she used them only once and left them frozen for a month before the second use--so she began aliquotting them and pulling out only what she needed. She had no explanation for the dropoff in efficacy; she just figured they were less stable than her other sets.
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Confusing bands from PCR
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