Hey Mark,
This is answered in the FAQ: http://wyday.com/wybuild/help/faq.php#where_vnum
The problem is that likely something is "rolling back" the client.wyc. Is it the customer? Is it you? Is it some other installer? Is your installer misconfigured (see the step-by-step walkthrough: http://wyday.com/wybuild/help/walkthrough.php, specifically step 5b -- it's important).