I agree with Sam, it doesn't make sense in every situation that all files be checked. There are situations where each update might have lots of files, or some really large files - which is where WyUpdate is truly powerful. The main reason this product has so many satisfied users (despite the prolonged delay in 2.6.15 ;P ) is that it is extremely easy to use and the updates are tiny, which means the end users are really happy as well. If every single file was checked, that would unnecessarily slow down the process. (hashing large files/lots of files is a cpu-intensive process).
If you really need to verify that all files are as expected, you could easily write a small program to verify that for you. If they aren't then just show the users a message asking them to stop messing with the files and install the program again.
On a side note, Sam, it might be helpful to add a command line parameter to WyUpdate which forces it to use the 'All to X.X' patch instead of the delta patch, so that it would be easy to fall back to that if needed.