Not sure if this is your problem altogether since I haven't tested the code, but the lines...

if($b[$x]=="***Begin $subject"){
while ($b[$x]!="***Begin Here***\n"){
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s/b

if($b[$x] eq "***Begin $subject"){
while ($b[$x] ne "***Begin Here***\n"){
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When you are comparing strings, eq and ne are the operators. Numeric operators are == and !=.

Again, I'm not totally sure this is your full problem, but I know when searching strings, == and != will give you unpredictable results.

Also, if your line will not always be the exact same string... ***Begin $subject Then you might want to try a regex...

if($b[$x] =~ /\*\*\*Begin $subject/){
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Good luck.