Further study of this naughty case reveals no problem in the FFT code. Unfortunately, the FFT data number being squared does not exhibit "random" properties that generates low round-off errors.
I'm talking to the PFGW folks about possible workarounds. They have seen this many times in the past. Since prp3 does the last 50 squarings with round-off checking enabled, then I think it is safe to use. If you get this error in the last few iterations, I'll bet you have a probable prime and the next rev of prp3 will backtrack and handle properly.
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