It's even worse than I thought initially. It turns out that the error is systematic and not sporadic (as I should have immediately guessed from its repeatability). It turns out that there is always a sort of inflation of the values of the sum of squared differences coming from somewhere.
This means that while the script looks like it is working great and doing what it should, it is completely bunk and will need to somehow be fixed to avoid this issue. I am thinking about trying to put a series of commands in to reset the values of different variables to zero in hopes of clearing out whatever error is compounding on me.
The next option if that fails it to post the relevant files to the R mailing list and hope someone is kind enough to tell me where I went wrong . . . which I somehow doubt.
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