Sync'd Analog In and Digital In

Hello,
I am a new LV user and am having difficulty with my vi. I'm attempting to use a PXIe-6361 to output hardware timed digital bytes for external multiplexer control for channel select, and then do an analog read of that selected channel. The clock used to control the digital output is synchronized to the analog in read and is running at speeds ranging from 20kHz to 100kHz (manually adjusted in between executions). When this system is running the scope shot looks good (See below...A2 is trigger for AI, and bit lines are the digital mux addresses).  The issue I am having is related to filling an array with the samples collected from each channel and replacing them each time they're sampled.  The read of the digital output value used for an array column pointer to replace older data does not appear to stay sync'd and causes the data to jump around among various array columns.  The VI is attached, any ideas for a fix out there?
Attachments:
Address Scanning & Measuring_single loop.vi ‏98 KB

I just added the Input Buffer vi, set it to 5000 and still see the error.  Seems the error is related to the time to collect triggered samples. I am running at 2MHz sample clock rate and when the sample size get sets to approx 50 or smaller the error shows up.  This would be when the total sample time is 25uS or faster. 
Attachments:
Buffer Error.png ‏20 KB

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    Attachments:
    method export signal.vi ‏21 KB
    method connect terminal.vi ‏36 KB
    Send a TTL pulse.JPG ‏288 KB

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