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.