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