On the 7344 there are no "factory defaults" stored in a ROM on the board. So if there is a chance that someone could change your settings in MAX you should set all necessary parameters in your program.
Here you can find a complete initialization routine written in C. It's written for NI-Motion 4.5 so you may have to do some minor modifications to adapt it to the API of NI-Motion 6.1.3 (current version).
You can still use MAX to test your settings and use the parameters you have found to be suitable in your C/C++ program.
Best regards,
Jochen Klier
National Instruments Germany