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Differences in CIN management between Labview 5.0 and Labview 7.1 ?

Hi,
 
I'm using a VI on a two photon microscope. It steers the laser beam in the sample (quite the same way as a TV scan, scanning a fast line on the X axis, then moving the line down) controlling two mirrors by the PCI-MIO-16E-4 Multifunctions card on traditional DAQ and at the same time it serves as the acquitision through a non-NI DSP Multifunction-board with on-board buffers and hight data throughput (70 Mb/s).
 
It is this part of the program which gives us strong headaches since we have upgraded to a new PC.
On the old machine we used Win2k and Labview 5.0; on the new machine we planned to use WinXP Pro and Labview 7.1.
The acquisition part of the VI uses 2 CINs. One is used to configure the FPGA on the Multifunctions board at initialization.
The second CIN reads he buffers received from the board and puts them into the shape of an image.
 
Now since we tried in WinXP Pro and Labview 7.1, we get some kind of weird bugs. Either there is a big problem concerning the synchronization of the mirros with the acquisition or with the image reconstruction. We have already tried :
 
1. Putting everything back into the old machine to verify there has not been any damage to the boards. OK
2. Using the boards in the new machine but with Win2000 and Labiew 5.0, just to be sure that there are no conflicting elements in the hardware. OK
 
As we wanted to check everything slowly but surely we then installed LV 7.1 on the new machine but still with Win2k. And here the problem appears !
First we thought the drivers for the Multifunctions board (ATEME Adr128C6x) were not compatible with WinXP Pro, so at this point we were quite surprised to notice the problem seems to be caused by the upgrade from LV 5.0 to 7.1 !
 
Now, finally my question is : Are there any major changes in how Labview handles CINs between LV5.0 and 7.1 ?
Can the
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