Disk Utility encryption vs. FileVault 2

I'm doing a clean install of Lion onto my iMac and I would like to have full disk encryption.  I'm booting to a Lion DVD and have just zero wiped my hard drive as "Mac OS Extended (Journaled)".  I see an option for format as "Mac OS Extended (Journaled, Encrypted)" and was wondering if there are any differences or advantages/disadvantages to encrypt the boot disk in Disk Utility rather than FileVault 2.  During research of FileVault 2 I discovered a drawback; one must shut down the computer to take advantage of the encryption:
From Macworld:
http://www.macworld.com/article/162999/2011/10/complete_guide_to_filevault_2_in_ lion.html
"While your Mac is booted, anyone with physical access to the computer—someone who sits down in front of it, breaks in remotely (however unlikely that seems at the moment with a Mac), or runs away with your laptop—could access your data. So get used to shutting down your Mac when it's not in use, or when it's out of your control, rather than putting it to sleep."
Any info much appreciated!

Update: I called Western Digital and they say this error is caused when one of the sectors of the hard drive is damaged in some manner (they didn't elaborate, but I assume it's some sort of physical corruption). So, if you have the same error, chances are you'll need to replace the drive.

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    Dr. Smoke
    Author: Troubleshooting Mac® OS X
    Note: The information provided in the link(s) above is freely available. However, because I own The X Lab™, a commercial Web site to which some of these links point, the Apple Discussions Terms of Use require I include the following disclosure statement with this post:
    I may receive some form of compensation, financial or otherwise, from my recommendation or link.

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    Author: Troubleshooting Mac® OS X
    Note: The information provided in the link(s) above is freely available. However, because I own The X Lab™, a commercial Web site to which some of these links point, the Apple Discussions Terms of Use require I include the following disclosure statement with this post:
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