It sounds like you may not be using the SI Estimate ARX Model.vi correctly. If you look at the help for this VI, it describes the inputs it is expecting. If it's the case that the single value you receive for your response is the same throughout the entire 128 sequence of uniform white noise stimuli, then you could create an array of 128 elements using the Initialize Array.VI. However, you should consider whether or not a single point response actually represents the complete response to the input signal. In other words, does a single value held over X amount of time represent the response to your input over X amount of time (128 elements), or do you need to sample your response longer?
I hope this helps. Be sure to take a look at some of the shipping examples for the System Identification Toolkit as well in Help->Find Examples.
Regards,
Kristi H