I have not run two programs in different environments like this but I do have some concerns. The NI-DAQ driver is not multithreaded. Do to this fact alone I am concerned about the integrity of your acquisition. Take a look at how your calls are made. For example, if you are doing an AI read, it will block any other calls to the driver until that AI read is done. If you can guarantee that the calls will not overlap you shouldn't have an issue but I doubt you can guarantee this.