Forgot to mentioned, I have use strict;

You should also be using warnings (or -w) because then you would see:

Variable "$targetSheet" will not stay shared at - line 46.
Variable "$row" will not stay shared at - line 47.
Variable "$col" will not stay shared at - line 47.
Variable "$group" will not stay shared at - line 47.
Variable "$assert" will not stay shared at - line 47.
Variable "$ftest" will not stay shared at - line 47.
Variable "$mergeAcross" will not stay shared at - line 55.
Variable "$mergeDown" will not stay shared at - line 59.
Variable "$isComment" will not stay shared at - line 62.
Variable "@str" will not stay shared at - line 63.
Variable "$isData" will not stay shared at - line 63.
Variable "$targetSheet" will not stay shared at - line 68.
Variable "$isComment" will not stay shared at - line 73.
Variable "@str" will not stay shared at - line 77.
Variable "$hvp_col" will not stay shared at - line 78.
Variable "$col" will not stay shared at - line 78.
Variable "$grp_col" will not stay shared at - line 79.
Variable "$ass_col" will not stay shared at - line 80.
Variable "$tst_col" will not stay shared at - line 81.
Variable "$plan_row" will not stay shared at - line 82.
Variable "$row" will not stay shared at - line 82.
Variable "$group" will not stay shared at - line 83.
Variable "$assert" will not stay shared at - line 84.
Variable "$ftest" will not stay shared at - line 85.
Variable "$isData" will not stay shared at - line 88.
Variable "$targetSheet" will not stay shared at - line 94.
Variable "$isData" will not stay shared at - line 95.
Variable "$isComment" will not stay shared at - line 95.
Variable "@str" will not stay shared at - line 96.
Variable "$func" will not stay shared at - line 101.
Variable "$compl" will not stay shared at - line 101.
Variable "$group" will not stay shared at - line 101.
Variable "$assert" will not stay shared at - line 101.
Variable "$ftest" will not stay shared at - line 101.
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And resolving those would go a long way to explaining the problem you describe in the OP.

bart's comment on closures is exactly the reason for your problem. See this simplified example:

use strict;
use warnings;

sub func {
    my $calls   = shift;
    my $strange = "Call $calls";
    print "In func (start): $strange\n";

    sub subfunc1 {
        print "In subfunc1: $strange\n";
        $strange .= " even";
    }
    
    sub subfunc2 {
        print "In subfunc2: $strange\n";
    }       

    subfunc1();
    subfunc2();

    print "In func (end): $strange\n";
}

func(1);
func(2);
func(3);
func(4);
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which creates the following output (including a couple of warnings!):

Variable "$strange" will not stay shared at closure2.pl line 10.
Variable "$strange" will not stay shared at closure2.pl line 15.
In func (start): Call 1
In subfunc1: Call 1
In subfunc2: Call 1 even
In func (end): Call 1 even
In func (start): Call 2
In subfunc1: Call 1 even
In subfunc2: Call 1 even even
In func (end): Call 2
In func (start): Call 3
In subfunc1: Call 1 even even
In subfunc2: Call 1 even even even
In func (end): Call 3
In func (start): Call 4
In subfunc1: Call 1 even even even
In subfunc2: Call 1 even even even even
In func (end): Call 4
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which clearly demonstrates that the variable $strange in the subfuncs is decoupled from $strange in func in the second and subsequent calls to func. The warnings also tell the same story.

UPDATE: Compare to the following:

use strict;
use warnings;

my $strange;

sub subfunc1 {
    print "In subfunc1: $strange\n";
    $strange .= " even";
}

sub subfunc2 {
    print "In subfunc2: $strange\n";
}       

sub func {
    my $calls   = shift;
    $strange = "Call $calls";
    print "In func (start): $strange\n";

    subfunc1();
    subfunc2();

    print "In func (end): $strange\n";
}

func(1);
func(2);
func(3);
func(4);
[download]

whose output is probably what you expected. Whether or not this is good style is a diffent question ...