I see this problem, too
I know this doesn't help, but I'm having the exact same problem.
I'm developing an iPhone app, and using Hudson to do nightly builds. So, one of the artifacts is my .ipa file.
If a Firefox user goes to my webpage and downloads the .ipa, everything works fine, the file's name ends in .ipa.
If a do the exact same thing in Safari, my app is now named "myapp.ipa.zip"
Just dropping the .zip from the end of the file name fixes my problem. This is annoying, though, because I need special instructions for my testers. If they double-click this file, then it will get unpacked. Now I need to say "If you download with Safari, be sure to turn off automatic unpacking, and also rename the file when you are done"