ak,
Actually, the 1kHz source is generated by the operating system (in this case, Windows), and as such isn't a "hard" timing source that can be trusted to be deterministic. The 6514 doesn't have any hardware timing on it (many of our other DAQ boards do, such at the M-series), so your timing performance is entirely dependent on your system. The Timed Loops are definitely your best option in this scenario.
The 1MHz clock option is only available on the LabVIEW Real-Time operating system, which IS a CPU-generated clock that is passed through by the operating system.
--Paul Mandeltort
Automotive and Industrial Communications Product Marketing