I'm also running your version of OS X Lion and use Time Machine for backups.

I get the nagging feeling from your description that your OS and/or Time Machine app might be at fault — not Time Machine HD, especially given your last comments.

How about booting into Recovery HD and running Repair Disk — first on your iMac's HD and then, if that doesn't solve the impasse, on your Time Machine HD — from there? If it works, it's a cheap and easy way out.