Dear Dave
Im sorry to hear of your problem. i cant say that we have exactly the problem that you describe but we have had sufficiently similar problems that we often go back to Southerns to sort out PCR dilemas. As you well know, from the Spudich Myosin paper, Campbell recombination occurs at a finite rate so your explanation sounds feasible and could be checked by high resolution Southerns.
Belated Happy New year and I hope it sorts out for you soon
Jeff
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