Could you please implement in wyUpdate that if file copy operation fails that it goes to sleep for one second and tries again (maybe this should be repeated several times if it fails again).
wyUpdate already does that when the file is in use. This is something different -- it sounds like your user is elevating to a non-admin user. Or maybe they're elevating to an "admin" user that someone stripped of admin powers using the Group Policy Editor.
Did wyUpdate ask for UAC elevation? Are you running as an admin user or an elevated user (i.e. do you have UAC turned off)? Does the update ever succeed?