Sometimes the process on which you press hotkey for TWD, does not do any process, but call some other process. Since TWD watching the first process, it assumes that it is done. So may be CT is calling some other process, may be in it's own folder, to do the time consuming job. You can run some process viewer/explorer to check it.
I have plan to allow user to change or select the actual process which is doing the job. Hopefully will be able sit with it in next year.