Encoder Counter Intermittently Set to 0

Question

I am using Labview on a windows XP box with a 6221 DAQ board connected to a 7330 motion controller via a RTSI bus.  I believe I have everything roughly working, but there is a behavior that I would like to explain before I go live.
I am sampling an analog input in lock step with a counter that is fed by the encoder signal from the motor.  So I have a series of 2 numbers that I record to file, and the sampling starts at the same time, the sampling is done by the same clock.  This all seems to work.
If I look at my series of #s regarding the counted ticks that the counter has generated from the linear encoder task that I set up to keep track of the encoder position, I'll get what I expect, but once in awhile there will be a 0 stuck in there.
For example:
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
0
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
I cannot seem to discern when this happens and when it does not.  My first guess is it has to do with motor speed/acceleration and sampling rate of the DAQmx Create Channel T(AI) I used to sample the analog input which is the same sample clock that is used for the DAQmx Create Channel (CI-Position Linear Encoder), but I have not had this behvior be reproducible based on sampling frequency or motor speed.
I appreciate any ideas.
Thanks

Answer 1

Sorry for the delay, I've been working on other items.
  OK so as I understand it you are trying to control a stepper motor (based on that's what the 7330 does) and you have it in closed loop (which is why you have an analog and digital signals) and are reading back the analog and digital position data. 
Clarification: I am reading the digital position data from the encoder and analog voltage from a force transducer that will vary over the course of the movement (the force will be all over the place during move)
Both of which are being read back by the 7330 and then the digital signal from the encoder you are passing via RTSI to the DAQ board and that is where you are reading and recording those values. 
Further Clarification:  Only the digital encoder signal goes back to 7330 and then is routed over the RTSI. The analog signal goes striaght into the DAQ.
                            Additionally, the digital encoder signal gets routes over RTSI to PFIs 8,10,9 that are counter 0's inputs.  I then set up a DAQmx Create Channel (CI Linear Encoder) event to sample the counter in step with the analog input.
    I guess it would be pretty hard to see if there is a missing pulse looking at the TTL signal on the 7330's user defined digital lines...but what if you wire the siganl directly up to the DAQ board? any change?
Have not tried, and probably won't (I'll explain why I won't try below)
and in your example the count goes from 12 to 14 and there is the 0 where 13 should be...is this always the case? does it keep the correct count? and is it always at the same number? 
       The count doesn't skip #s, it just goes 12 12 12 12 0 12 12 12 13 13 13 14 14 14  (I need to check this behavior more, will do that next week)
       Count is correct
       Not at the same #
       -Since there is no # skipping, or I can just interpolate what 0 should be, I'm hesitant to rewire things.
Also, does the analog signal have anything to do with the digital signal you are sending to the counter (other than that you want them to have the same sample clock)
    The signals have nothing to do with each other at this point because I am just debugging the system with a fake input
Seeing that I am sampling a counter, all I can think of is that there is a mismatch somewhere in the counter sampling event.  That is to say, the counter value is always at a value, when it gets latched and how many times it is sampled and how many times I read it out might give some mismatch where I think that I have recorded X events, but because of timing, only X-1 samples have made it into the buffer?  Could it be something like that, that would be my only explaination of why a 0 gets in there, because as I said I am sampling a counter.
Thanks