Finite Pulse Train TIO-Timing Specs

Howdy everyone,
Got a question regarding the pulse specs of finite pulse generation with a 6602 (TIO chip).
I'm using a slightly modified version of the Finite Pulse Train (NI_TIO).vi found in the examples directory to produce finite pulses.
The slight modifications are to allow for some hardware triggering.  I am using counters 2 and 3 to produce a finite pulse train.
My external electronics provides the trigger to the gating counter.
I want all of my timing specs relative to this external pulse.
Let's say I want a delay of 10 seconds until my first output pulse is produced by the output counter; I want pulses to come every 1 sec; Pulses are 0.5 sec wide.
I know from looking into the VI's that the TOTAL delay--ie the time from my external trigger until the time the output counter outputs a 0.5 sec pulse--is equal to the "initial delay (in secs) in the finite pulse specs cluster in the VI plus the interpulse interval minus the pulse width.
Thus, If I enter a value of 10 seconds for initial delay, I actually expect the first pulse to be output at time = 10 +1 - 0.5 sec = 10.5 sec.  This is one-half second later than desired, but it is easy to correct.
Now for my real question: 
I'm usually looking at pulses coming about 20 msec after the trigger arrives.  The pulse interval is 5msec and the pulses are 0.5 msec wide.
 Even when I program my counters to get the timing I want with this correction, ie. implement the formula Desired Delay = "Initial Delay" - (pulse interval - pulse width), I still see my pulse arriving late by 1msec.  1 msec is enough that I care to get it right.  I don't understand the source of this delay.  Does anyone have any idea what could be happening?
It seems totally independent of any parameters I enter for pulse interval, intial delay, pulse width. 
Not sure if it matter, but I'm generating this finite pulse train inside of a much larger VI that is busy collecting and displaying data from a 6071E.
Any thoughts/help would be greatly appreciated!

I'm using Traditional DAQ (not DAQmx), so I think points 3 and 4 are not strictly true for my VI.
(I'm am very hesitant at this moment to think about switching over to DAQmx :  I"m at the end of my graduate career and don't have the time to overhaul my program at the moment; and my VI works perfectly for my needs..except the 1msec delay.  I'll suggest future lab peoples move to mx...)
As I understand, for traditional DAQ:
1. Start the counter -- I believe it will force the output into its idle state (low by default).
2. Trigger edge occurs
3. Output remains in idle state for "initial delay."
4. Output transitions to armed state and remains low for "low time" which is computed/specified by the "frequency" and "duty cycle" specs.  So the total delay is the "initial delay" + "low time"
5. Ouput transitions to high state for a time, also determined/computed by the frequency and duty cycle specs.
6.Thereafter, the times will be based on your regular pulse specs, such as low time / high time.
OK, I didn't want to drag the VI into it, but it seems there is no other way; and I really want to know why my timing is not quite as I would expect.
The VI I posted has 3 outter sequence frames.  The action, as far as we're concerned in this post, is in outter frame number 3; inner frame number 3, case True, subVI Finite Pulse Train (NI-TIO)-jev4.vi.  This VI is "slightly" modified from the example that came packaged with LV "Finite Pulse Train (NI-TIO).vi"  The modifcations I made were 1. removed the while loop that checked the status of the counters, because I needed this subVI to return before the pulse train had actually finished executing.  2. Added start trig capability to the gating counter's gate.  (Maybe  this is the source of the 1msec error?).
There is a variable "stim delay (msec)"  that specifies when the first high pulse should be output from the 6602. (device 2  for me.)
To complicate things further, " stim delay" is actually relative to another variable in Neurochip-legacy.vi called "record delay."  Record delay specifies the delay between the the arrival of the trigger pulse and start of data acquisition on NI6071E.  (had to do this because of the way things are set up in the lab).  This trigger pulse  is shared with the 6602--it is hardwired in a breakout box to also be routed to my 6602 card.  Thus, if the trigger arrives at time = 0, record delay = 20 msec, and stim delay = 40 msec, I would like to see my first output pulse of the train (on the 6602) come at time = 60 msec.
For the time being I have set the "initial delay" = record delay + stim delay - (pulse interval - Ta), where pulse interval is just 1/"frequency" parameter for finite pulse generation, and Ta is the desired width of the output pulse which in turn specifies "duty cycle" parameter.  For the moment, I've also hardcoded in a 1msec correction--which was the whole reason for the original post.
Maybe in all this arithmetic and wiring I've made a goof somewhere...if so, maybe a fresh pair of eyes would help.
Ok, so if you are brave enough to check out the code,  it is attached.
If you find that you are getting the same result as me, I would love to know it.
If you are getting different result than me, I'd love to know it.
If you see where I went wrong, I'd really love to know where.
Thanks very much
jon
Attachments:
Neurochip-Legacy.vi.zip ‏637 KB

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