Brad,
If you are using DAQmx 7.4 or later, your m-series card supports programmable power-up states. If you go into MAX, right click the PXI-6229 and select properties, there will be a tab called "Power-up States." It is recommended though that you do not change these states often because the EEPROM has a limited number of read and writes. Have you tried this feature for your application?
Regards,
Jeff Tipps
Applications Engineer