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why it count when it should not (Buffered Period Mesurement)

Hi!
 
I have a 6602 DAQ card that uses as a counter, it synchronize with a laser scanner (stand alone application).  I want the program to work this way: When the scanner start scan a line it will set the sync channel to high and the counter start to count, when the scanner has reach the end of the line it will turn to low and the counter stop. It will do the samme thing in the next line until a hole page has been scanned.
To scan a line it will take 0,7 sec and the counter period is 0,01 sec which a line will give 70 samples, the values from a line is a vector and hole page become a matrix.
I want to able to start the LabView program first and wait for the program from the scanner, that's why I have a while loop outside the case loop.
 
My problem is: It give too many lines, for example the scanner scan only 2 lines but I get 5 vector instead of 2.
 
My (problems) quetions are:
1) Why does it give the values even the condition to stop the inner while loop is met?
2) The larger time difference between LabView program start to the scanner program start will give more vector. For example, the signal to the case loop is low then it don't do anything until the signal is high, if the time difference (between low and high) is big then it give more vector which is inaccurate.
 
I hope someone can help me with this.
 
Best Regards,
 
Giang Vu
 
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