Hi Cam,
"What dictates this" is something you can prevent actually, and yes you can carry out this process manually if you wish. Let me explain...
What dictates is database corruption or the program thinking things are corrupt occurs when Trainz TS12 is not shutdown properly. When TS12 has been shutdown unexpectedly or you've restarted your computer before the program has completed updating, TADDaemon, or the database server built-into Trainz, doesn't know the status of the files. So rather than just launching the program, and working with corrupt data, the TADDaemon will start verifying the data and checking the tables before it allows the program to start up. As you've found out, this process can take some time.
Shutting down improperly isn't always your fault because the program continues processing, closing files and shutting down files in the background, after the program closes its interface. The way around this verification process is to wait about 5 minutes after closing Trainz before turning off or restarting your computer.
To initiate the process manually, go into Content Manager and choose Quick Database Repair (QDR) from the File menu. If there are extensive problems, such as program crashing, you need to sometimes run an Extended Database Repair or EDR. This is a lot more extensive and the process can take forever. Due to some things caused by this process, this is recommended only as a last resort when nothing else fails.
Hope this helps.