Are you getting warnings when you build the updates? If so, listen to those warnings. They're important. My guess is that you're adding the same file to multiple versions in wyBuild. So, when wyBuild compares the files, and it sees the same file, there will be no patch generated. Why? Because the file on the disk is unchanged.
Short answer, follow the step-by-step walkthrough: http://wyday.com/wybuild/help/walkthrough.php
Longer answer: follow that walkthrough, and pay special attention to when it says "Create a folder to store the files for this new version (we're calling it 1.2).".
Create a new folder for every version of your app. Put the files specific to those versions inside each folder. Then add those files from the folders to wyBuild.
Does that make sense?