There is a growing interest on measuring time intervals between the J peak of the ballistocardiogram (BCG) and several features of other cardiovascular signals such as the ECG in order to obtain cardiovascular function markers. Nevertheless, possible uncertainty factors involved in these measurements have not been identified and analyzed, which is a necessary step to advance towards standardization in this reemerging biomedical engineering field. In this paper we analyze the effect of the low-pass cutoff frequency and phase characteristic of filters, noise and power line interference on J-peak time measurement. We conclude that BCG acquisition systems require a minimum low-pass cutoff frequency of 25 Hz but the phase angle of filters at this frequency introduce more than 6 ms delay that increases with increasing filter order. Further, SNR and power line interference levels respectively below about 25 dB and 30 dB, commonly found in data acquisition systems in this area, may lead to uncertainties in the time position of the J peak of tens of milliseconds, which are comparable to measured time interval changes that may have diagnostic interest.