Hello Volkan,
I looked at your VI and used it with many different signals (PCI-6251). It worked great. I didn't get any transient responses. Could you please run the attached VI and test only one channel and gradually increase the number of channels used to see the response. The M series card has the capability of sampling up to 1.25MS/s, so when using 4 channels, you could sample up to 312KS/s. You should not be seeing this clipping with the sampling rate you are using (20KS/s). Please monitor the signals that you are feeding into your DAQ card with a scope to see if the signals are clipped. Also, please check test the different channels in MAX to see if each channel is functioning properly. A test of your task should reveal if any of the channels is malfunctioning.
Thank you.