I recently stumbled across a bug in the Time Machine utility in Mac OS X. It seems that whenever you run, through the Disk Utility application, a "verify disk" command, Mac OS X is subsequently unable to backup changes in Time Machine. The worst part is that Time Machine will continue to work just as usual but it will simply not backup changes made on your source HD to the destination HD. The only solution I found to this problem is to make a whole new Time Machine backup. As it unfortunately defeats the purpose of using Time Machine, I'm basically back to cloning my hard drive using Super Duper.
Apple is aware of the problem but no fix has been made available yet.
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