clickonce problem

I also ran into this problem.  I encountered the problem after moving my clickonce app to IIS6.  In windows XP (IIS5) it seems to work out of the box.  Anyway, after hunting around I was able to get it working.  I had to add MIME types for the offending files.  You can access the MIME types by going into your site's properties -> HTTP headers -> MIME types -> click NEW....then add an extension and MIME type.

I added these to get it working

extension: msp
MIME: application/microsoftpatch

extension: msu
MIME: application/microsoftupdate

After doing this my .Net 3.5 prerequisites installed fine.

Hope this helps someone...