Look at the precedence of operators, =~ is of higher precedence than ... So $record=~ /^start\b$/ .. /^end\b$/ is interpreted as (scalar $record =~ /^start\b$/) .. (scalar /^end\b$/) (in this case the scalar keyword doesn't change the result, so you can pretend they are not there to make it clearer). So you actually have: (scalar $record =~ /^start\b$/) .. (scalar $_ =~ /^end\b$/) because match operations work on $_ by default.

while (<CHECKBOOK>) 
{

     if (/^start\b$/ .. /^end\b$/)  
     {
          print MYOUTFILE "$file;$_\n";
     }
}
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should work better. Or $record =~ /^start\b$/ .. $record =~ /^end\b$/ if you want to use $record, but that looks more noisy.