If you add the line: 
print join ' ', $atob, $btoc, $atoc, "\n";

[download]
You'll notice that $atob is -2.5, $btoc is -0.5, and $atoc is -3.

For clarity, I'd also use the abs function rather than nested logic: 

if (abs $atob > 1  &&  
    abs $btoc > 1  &&  
    abs $atoc > 1     ) {

    print OUTFILE "DIFF > 1 all three\n";
    $matrixflags[$row - 4][$i] = 1;
    $matrixflags[$row - 3][$i] = 1; 
    $matrixflags[$row - 2][$i] = 1;
}

elsif (abs $atob > 1  &&
       abs $btoc < 1  &&
       abs $atoc > 1    ) {

    print OUTFILE "DIFFA > 1 $atob  $atoc $btoc\n";
    $matrixflags[$row - 4][$i] = 1;
    $matrixflags[$row - 3][$i] = 0;
    $matrixflags[$row - 2][$i] = 0;
}
elsif ( ... ) { ... }

[download]
And like the other monks suggested, use strict; and use warnings; will point out where your code could run into problems. There is also use diagnostics; for an extra helping of advice.

In reply to Re: if logic OR parentheses problem by gamache
in thread if logic OR parentheses problem by Ellhar

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