Usually a time spectra is related to some trigger signal that is input to a AUX input to reset the time counter. Note that the counter counts down from a preset value, so it is essential to enter a preset value for the time counter that is larger than the greatest time of interest.
In the latest MPA-3 software that can be downloaded from our website is a new method implemented to get time spectra without AUX input. Here is part of the readme file describing the news:

MPA-3 Server Version 1.84 (Apr-01-2010):

• A new mode "Time Differences" is possible for time spectra using the RTC or 1 msec realtimer. So you can now record an absolute time for each event using "Software   only" as "Preset Load Mode" in the RTC dialog. The "Preset" must be longer than the time of your acquisition. Using "Time Differences" in the definition dialog for time spectra you can then record time spectra relative to a reference to an event in any selected ADC, also in replay mode. The time of the next event in the reference ADC after the end of the time spectra is used as a new reference time.