Can anyone help me? Trigger camera acquisitio​n​n with RTSI connection

Hi all,
I've posted this in two other forums now and have gotten no responses so here's my last try.
I am having sync issues with my code.  I wish to generate a certain number of samples - these correspond to raster scanning mirror positions.  However, I also have a optical switch (PCI-6731) and camera (PCIe-1427) in the code.  For each mirror position, I want to switch my optical switch and capture a camera frame.  Seems simple enough but in practice it's proving frustrating!!
In an effort to sync everything, I outputted the CO.Pulse.Term to
(1) RTSI0 channel (camera) and to
(2) Ctr0Out which my switch is connected to. 
I have used the IMAQ Generate Pulse.vi to trigger the camera.  I know that my board does not have an RTSI frame trigger so in MAX I set Trigger Mode to 1 (Internal), Trigger Source to CC1, I have unticked the CC Lines source box and CC1 is set to External trigger 0.  I connected my two boards with an RTSI cable. 
Originally, I was grabbing triggered images and putting them in a folder but they were completely out of sync with the switch and took a long time to capture.  I decided to grab the frames and save them to .avi instead and then split the frames afterwards.  But I am still having sync issues.  I tried to put in the IMAQ ConfigureTrigger3.vi to configure the action to trigger each buffer but I kept getting timeout errors so I removed it.  The .avi capture is within a while loop, set to stop when is equal to the number of original samples (i.e. positions) I set.
Why is there a sync issue with the switch and camera acquisition if both are determined by the same sample clock rate?  Does anyone have any insights?? Apologies for all the cross posting but I am desperate to get this up and running.   Please see the attached code.
Miika
Attachments:
Galvo3D new redo 3 avi.vi ‏112 KB

Hello Matt
Thank you for your reply.  I tried all that you suggested but nada! Nothing worked.
So I brought the Sony Camcorder back to the store (as it was brand new a couple of days old) and exchanged it for a Canon Legria HF R206 HD.
I can now easily upload the video and photos from this camcorder onto my MacBook and it all works fine that way.
But my MAIN PROBLEM is that iMovie in my iPad2 can't read the content of the camcorder using iMovie?
I'm wondering if it has something to do with the fact that I'm using a different version of iMovie on the MacBook vs the iPad 2.  Everything works fine using version iMovie 09 ver. 8.0.5 (820) on the MacBook.
I'm using iMovie version 122 ( 2010-2011) on the Ipad2.
After going back to the store and dropping an extra 20 Euro as I was advised that this Camcorder does work well with all Apple products, I now find that it may be the version of iMovie that is preventing the upload to iPad2.
Can you shed any of your wisdom on this for me please?
Many thanks
Aryelle

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