Update: davidrw's response above is much simpler. I was responding to the algorithm as posted, and pointing out that your inner loop needed some work :)

You should probably restructure your inner loop, and pull the GenerateTestFileList() call outside of it.

my $count = 0;
foreach  (@keywords) {
  if( ($_ eq "database.txt") || ($_ eq "keywords_database.txt") ) {
    print "Found $_\n";
    $count++;
    last if($count == 2);
  }
}
if($count != 2) {
  print "At least one database is missing.\n";
  GenerateTestFileList();
}
[download]

I would also recommend using the string equality operator (eq) instead of regular expressions. You know exactly what the files are named, and you don't want an accidental match. For example, the strings "random_database.txt" and "some_other_database.txt.tar.gz" will match your elsif(@keywords[$kdbase] =~ /database\.txt/) line above.