Well,I think thedifference occurs well before comparison block started on peak/average calculation stage.
If one wants to get further with this task one could just tweak threshold a little (threshold stored inside task itself) and this will makethe app reports more pulses.
That way even apps that report 10 pulses currently can report that 11th pulse too. So we can see what they calculated for this task.
The area of interest (in task header) is:

  <analysis_cfg>
    <spike_thresh>24</spike_thresh>
    <spikes_per_spectrum>1</spikes_per_spectrum>
    <autocorr_thresh>17.7999992</autocorr_thresh>
    <autocorr_per_spectrum>1</autocorr_per_spectrum>
    <autocorr_fftlen>131072</autocorr_fftlen>
    <gauss_null_chi_sq_thresh>2.46249485</gauss_null_chi_sq_thresh>
    <gauss_chi_sq_thresh>1.41999996</gauss_chi_sq_thresh>
    <gauss_power_thresh>3</gauss_power_thresh>
    <gauss_peak_power_thresh>3.20000005</gauss_peak_power_thresh>
    <gauss_pot_length>64</gauss_pot_length>
    <pulse_thresh>20.7340908</pulse_thresh>
    <pulse_display_thresh>0.5</pulse_display_thresh>
    <pulse_max>40960</pulse_max>
    <pulse_min>16</pulse_min>
    <pulse_fft_max>8192</pulse_fft_max>
    <pulse_pot_length>256</pulse_pot_length>
    <triplet_thresh>9.73841</triplet_thresh>
    <triplet_max>131072</triplet_max>
    <triplet_min>16</triplet_min>
    <triplet_pot_length>256</triplet_pot_length>
    <pot_overlap_factor>0.5</pot_overlap_factor>
    <pot_t_offset>1</pot_t_offset>
    <pot_min_slew>0.00410000002</pot_min_slew>
    <pot_max_slew>0.0203000009</pot_max_slew>
    <chirp_resolution>0.1665</chirp_resolution>
    <analysis_fft_lengths>262136</analysis_fft_lengths>
    <bsmooth_boxcar_length>8192</bsmooth_boxcar_length>
    <bsmooth_chunk_size>32768</bsmooth_chunk_size>
    <chirps>
    <chirp_parameter_t>
      <chirp_limit>30</chirp_limit>
      <fft_len_flags>262136</fft_len_flags>
    </chirp_parameter_t>
    <chirp_parameter_t>
      <chirp_limit>100</chirp_limit>
      <fft_len_flags>65528</fft_len_flags>
    </chirp_parameter_t>
  </chirps>
  <pulse_beams>1</pulse_beams>
  <max_signals>30</max_signals>
  <max_spikes>8</max_spikes>
  <max_autocorr>8</max_autocorr>
  <max_gaussians>0</max_gaussians>
  <max_pulses>0</max_pulses>
  <max_triplets>0</max_triplets>
  <keyuniq>-12226561</keyuniq>
  <credit_rate>2.8499999</credit_rate>
</analysis_cfg>

In particular, these 2 thresholds
<pulse_thresh>20.7340908</pulse_thresh>
<pulse_display_thresh>0.5</pulse_display_thresh>

If threshold will be lowered (I think first one should be used for changing reportable pulses), more signals will be reported.

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