Are you getting warnings inside of wyBuild when you build the updates? If so, read the warning. They're important.
My guess is that you're referencing the same files from disk in version 36 and version 47 in wyBuild. Meaning the files in wyBuild are referencing the exact same files on the hard drive -- and thus when wyBuild creates the patches it doesn't see any changes (because they are the exact same files).
Make sense?