I don't quite understand how you have things set up, but it sounds like you have "official" clocks and the cron job you're running get sthe time from them and resets the system clock. I have no idea how it could get out of sync unless your cron job is not working properly.

To answer your question, though, there is only one system clock in Unix. Calls to get that time are essentially direct calls to the OS. There is no other (standard) place to get time information.