Hi Ivanka,
If the two instruments are not synchronized or outputting at the exact same rate, then eventually the order will get messed up. You should be able to see a change of the "Bytes at Serial Port" right when this happens.
Do you have other commands available that starts acquisition of a finite number of samples and not infinite like in your case? Using finite acquisition the two instruments will be "synchronized" every time you give them the command to acquire.
Best regards,
Philip C.
Applications Engineer
National Instruments
- Philip Courtois, Thinkbot Solutions