One thing to consider is whether you want absolute time or relative time. If you think you are obtaining absolute time withing an interrupt handler with which to time-tag a data record going to disk, as an example, you need to consider that there is jitter due to operating system latency. You might want 1 millisecond accuracy, but jitter will give you some record to record skew, that might be observed as a small number of milliseconds difference, record to record.
If you are doing a short data capture, consider tagging your records either with an incrementing count, or get the start time and add a number representing your time interval to each recrod time stamp. I your sample timing is accurate, FIFO filling is accurate, and FIFO buffer interrupts are not lost, this method will produce very good time stamps without the jitter.
