Is the slowness you're encountering specific to Process Files steps with many files? If so, this thread discusses some reasons why using that will be slower than actions that process masks directly:
http://www.kinook.com/Forum/showthread.php?threadid=466
Please ZIP and send or post:
1) The info from Help | About | Install Info
2) The .bld file demonstrating the slowness (indicating which steps are slow)
3) A build log file
Thanks.