Lower trigger level,less peak found,what's wrong?

I am testing a NI5154 digitizer and the input signals are negetive pulses. I try to capture all pulses so I set a very small
trigger level, let's say 10mv, I am surprised to see much less waveforms captured than using a 50mv trigger level. Of course
when I try to increase the trigger level the found pulses will going down. The problem is what's wrong with small trigger levels?
I use a 1V vertical range and the digitizer is 8 bits. I also found these is a large difference when I change the trigger slop from
negetive to positive. As I understood there should no difference in the number of found pulses as the pulse will cross the trigger level any way.
Can anybody explain this? thanks a lot. 

Hello John:
I sent you a message but let me put it here again.
I am really too sad with with the trigger accuracy. This will destroy all our measurement because
the trigger accuracy will make our experiment not any precise any more.
Our goal is to determine precisely the number of pulse in a short window
and get the timing information of each detected pulse. So if the trigger
has such a large jitter we lose control of precision of the detected pulse.
Here I attached some figures which show how the pulses I captured look
like. I also attached the vi which I used to capture the signals. This
vi run the digitizer ni5154 to capture and save all the pulses in a cycle
model. A start trigger will start a new cycle measurement. Our goal is to
capture all pulses in a time window follow the start trigger.
The data got from a ion source is listed in the following.
trigger_level(mv) negative_slop_trigger positive_slop_trigger
5 20 8663
10 133 8399
15 750 8203
20 2828 7955
25 7344 7718
30 8600 7444
35 8367 7156
40 8068 7002
45 7835 6746
50 7631 6476
60 7060 6021
70 6642 5640
80 6168 5291
90 5807 4919
100 5413 4605
thank you for your help.
Attachments:
s2.jpg ‏34 KB
s1.jpg ‏35 KB
Copy of NI5154_run.vi ‏80 KB

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