If that is the case, then there is a bug in wyBuild.
wyBuild builds the updates to a folder on my computer, to test locally I created an IIS website around this folder, so all files created by wyBuild are left as is, yet the adler32 validation fails.
From what you are saying this should not happen.
How can I debug the issue?
Also, this issue is not visible until an update is run, could you implement the adler32 validation check within wyBuild so users will know patch updates are going to fail, before uploading all the updates to the server?