Autocorrelation of noise - negative correlation I am investigating autocorrelation of electrical noise as part of an undergraduate experiment (as detailed in http://physlab.lums.edu.pk/images/a/ab/Correlation.pdf). I sampled noise voltages using an 8-bit AtoD from a noise generator (whose description was not provided). I first sampled the noise directly, then I sampled it after passing it through a low-pass filter. I imported the data into MATLAB and used the autocorr function to autocorrelate it. The no-filter data autocorrelated as expected, being just 1 at t=0 (as in Fig 1 in paper); however, the filtered data decays initially as expected but then dips below 0 before coming back up and staying around 0 as in the image below. 

My three issues are:


I am not really sure what this means physically (is the correlation 'direction' changed so-to-speak?),
Why might this be occurring? I know that a description of the noise generator may be important here but I do not have that information myself.
Is there any way to correct this issue, and if not, what would be the best compromise?


EDIT:

Here are snapshots of the noise without and with the filter (RC=0.5ms) respectively:
If the impulse response of the low pass filter goes negative, that means that the filter is adding an inverted or negative image of the input signal to the output at that delay.  Which the autocorrelation is finding it as it is, negative.  The impulse response goes negative as one way of canceling out some of the input spectrum in the filter's stopband.