InstantUpdate it the ancient name of wyUpdate (it's the pre-1.0 name of wyUpdate). wyBuild has InstantUpdate.exe in the program's folder for backwards compatibility reasons with pre-1.0 versions of wyUpdate. When wyUpdate self updates it doesn't touch the filename, so you can name it whatever you want.
That being said, since v1.0, wyBuild has always built wyUpdate.exe (which is really just a copy of InstantUpdate.exe in the wyBuild folder).
Does this make sense?
Or are you saying a recent version of wyBuild produced InstantUpdate.exe when you clicked "Build wyUpdate"? Because that shouldn't happen.