What sort of carrier is your NI-9211 in? From your code, it appears to be in a USB cDAQ chassis (although it can also be used in an FPGA chassis). Assuming the cDAQ chassis, you should have hardware timing capabilities which will enable you to take data with hardware timed precision. Given your data rates, you could take it using the operating system, but the jitter on when data is taken could be on the order of 0.1s or more, depending upon what else is going on. Typical would be about 20ms to 50ms of jitter.
Lynn has already suggested one of the best ways to do this. Use a producer/consumer architecture (see the LabVIEW help for an example). The producer is your thermocouple reader, running at 1Hz read rate. The consumer is your logger. In the consumer, you log everything for the first time interval, then log only what you want after your intial inverval. Averaging points can be done in the logger, as well. It may be worthwhile using three loops - one to take data, one to process it by discarding or averaging, and the final loop to log. You could combine all this functionality into a single loop, since your data rates are so low, but I would not recommend it. Strange as it seems, it makes the code harder to modify and maintain if you need future additions.
Good luck! Let us know if you need further information.
