Are you using any type of signal conditioning on your signal? What NI hardware are you using to acquire the signal? A noisy signal may be throwing off your measurements. Here is a <A href = http://zone.ni.com/devzone/conceptd.nsf/webmain/01F147E156A1BE15862568650057DF15?opendocument>link</A> that may help you with that.
Russell G. Applications Engineer National Instruments