It can take up to three minutes for TADDaemon to finish after exiting Trainz. Best thing to do is call up the Windows Task Manager, tab to the processes page, look for the programme in the list and wait until it disappears.
Cancelling a rebuild not recommended as Trainz still won't open afterwards. Best case it will just run the process again when you next start Trainz, worst case you might brick your install and any work you've been doing.