All software, including Apache server is running under a user account. The specific user account limits the rights of software to access resources such as files or the network. Some "user" accounts are internal to Windows, though, and do not represent human users. Apache will likely run under such an internal account.
When you encrypt a file in Windows, you typically also restrict access to your own user account. As a result, other user accounts cannot access it anymore. Since Apache doesn't run under your user account (it works while you're not logged in, after all), Apache cannot access your encrypted files.
One easy solution is to turn on whole-disk encryption. This should be the default for laptops anyway; they're just too vulnerable to theft, loss, etc. You'll need a password to boot your laptop, but once it's booted the disk remains accessible to all software including Apache.
What encryption do you use? – cularis – 2011-07-08T11:00:39.090