It is a very difficult issue..
It has been ongoing since 7.6 firmware.. the issue hardly happens with 7.5 version.. the trouble is, I doubt your TC can be downgraded to that earlier firmware.
If you have applecare ring Apple and see if they can suggest a solution..
I would almost suggest for the moment the only way is a mechanical / electronic timer that reboots the TC at midnight every night. Crude but we were hoping Mountain Lion would fix several outstanding issues between TC and Lion.. it seems to have got worse.. much worse by the number of posts.