Time Machine glitch

I just checked Time Machine to restore a minor file, and discovered that it's not mirroring my current directory structure. New files and new directories show up in the "Today" screen, but not in the backup screens. WTF?

I have an alternate drive that I use occasionally for back up (for off-site storage). Have I confused Time Machine by switching from one to the other? I'm thinking I need to make a back up on the secondary disk, make sure it's correct, then wipe my primary back up drive and start over. Or is there a less drastic way to get Time Machine back in sync with my reality?

ETA: Does the procedure below sound reasonable? From an Apple discussion board

A4. Full Reset of Time Machine

a. Go to TM Preferences, turn TM Off, de-select the drive (select "none"), and click the Options button. Note any exclusions in the Do Not Back Up box, and other option(s) on that panel. Then quit System Preferences.

b. Eject, disconnect, and power-off the drive for a few moments, then reconnect it.

c. Delete the file /Library/Preferences/com.apple.TimeMachine.plist (in your top-level Library folder, not your home folder).

d. Go back to TM Preferences, re-select your drive, re-enter any exclusions and other options.

e. Do a Back Up Now or wait for the next scheduled backup.