Hi Raphael,
To address your questions re: the PCI 6221 M Series multifunction DAQ board:
1) The maximum sample rate of this board is 250 kS/s. This means that you are correct in that the maximum time between samples is 4 us. However, since you are collecting on 2 channels, the maximum rate per channel will be halved, so you will only be able to collect 1 sample per channel ever 8 us.
2) You don't need to create two separate channels for this acquisition. You can create 1 task, and add both channels to it simply by changing the channel string from "Dev1/ai0" to "Dev1/ai0:1".
There is a shipping example included with the NI-DAQ 7.4 installation which details exactly how you can do this.
The reason that you were not seeing samples Your code was not using a particular function to set the timing of the acquisition: "DAQmxCfgSampClkTiming".
To add a timestamp to your data, you could record the tick count at the beginning of your acquisition, and since you know the sample rate, it would be a simple task to correlate each sample to the initial start of the acquisition.
I have attached the shipping example for your perusal.
Good luck with the rest of your application!
Best Regards,
Evan R.
Applications Engineer
National Instruments
http://www.ni.com/support