Because your SQL statement isn't returning anything. Since it doesn't, then you never enter your while-loop, thus never entering the if-statement.

A few comments:

1. Don't print your HTML out in your Perl script. At the very least, use CGI's methods for creating HTML. Ideally, you'd use templates (a la HTML::Template, Template Toolkit, or Mason, to name a few).
2. Your SQL can very possibly break, if $company has naughty characters in it. I would use placeholders, if I were you. Something like:

   my $sql = <<__END_SQL__;
   SELECT DISTINCT name
     FROM master
    WHERE name LIKE ?
    ORDER BY name
   __END_SQL__
   
   # stuff here
   
   $sth->execute("%${company}%");
   
   # more stuff here
   [download]

3. You need to error-check your prepare() call as well as your execute() call. prepare() is where the SQL is checked for syntax. execute() is where it is checked against the database. A number of DBD drivers (such as Oracle) will dump out of prepare() if the tablename is wrong, or the like.

As for your actual problem, I would argue that you haven't through through what you want to do. I would build a list of $ag values within the while-loop. Then, outside the while-loop, I would check to see if you have any $ag values. If you don't, put your "Value not found" select. Otherwise, build the selects.