I often spell 'break' as last.

Beyond that, there's no need to stringify variables. If you want to set $exact_file to $junk_file, just do it. (If you're relying on overloaded stringification, it may be more clear to concatenate the assignee with the empty string. Luckily, you're not doing this, so don't worry about it. ;)

Other things... you're reading a file linewise, pushing each onto an array, and then comparing just the first two lines. Why not just read two lines?

Beyond that, it is good style to avoid indirect method calls (CGI::Cookie->fetch is much preferable to fetch CGI::Cookie), and calling subs with a leading ampersand and no argument lists *will* eventually cause you debugging grief. Use parens. Then drop the leading ampersand, as it's unnecessary.