I want to say that while you can see the files in Time Machine they may be part of an alternate backup partition and Time Machine knows this and is separating them from the current backup image.
Try these steps out to see if there is more than 1 disk with a Time Machine backup on it:
Tip: You can also browse the original backup drive for past backups by using "Browse other Time Machine Disks"--to see this choice, hold the Option key then click the Time Machine menu in the Finder (to see the menu, "Show Time Machine status in the menu bar" must be selected in Time Machine preferences.
From: Mac Basics: Time Machine
If so then load up the other image and try to restore the file that way.