The 5B47 is not designed for fast changing signals, which is why it has a 4Hz filter. The rise time for 80% of the full range is 0.2s (from the 5B user's manual
http://www.ni.com/pdf/manuals/321029a.pdf). A step response function typically has a lot of high frequency components, so a lowpass filter at 4Hz will tend to filter out all those high-frequency components and leave you with a distorted version of the original signal. If you need to measure fast changing signals, then I would recommend a measuring device that has a higher cutoff frequency. The SCXI-1102B, for example, is designed for measuring thermocouples and has a cutoff frequency of 200Hz.
Logan Kunitz
National Instruments - Austin, TX