Have you ever tried to save a file from web-based app or plugin, but the file doesn’t show up where you put it? Here’s why.
To prevent a malicious ActiveX or Java browser plugin from gaining access to your files and system, any file access gets blocked. So for example, when my QlikView browser plugin tried to save some business data as an Excel file on my desktop, the file actually went somewhere else:

My save location:
C:\Users\Shawn\Desktop\data.xls

Where the file actually saved:
C:\Users\Shawn\AppData\Local\Microsoft\Windows\Temporary Internet Files\Virtualized\C\Users\Shawn\Desktop\data.csv

This only applies to websites and plugins running in Protected Mode. Any website you add to your trusted sites zone will not be subjected to this security, which is why you should only add sites to your trusted zone if you truly trust the site with all your data.

Similar redirection applies to programs you run.  You can learn more about how IE Protected Mode and file/registry virtualization work to protect your PC on the Microsoft Developer Network site.