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TDC1000: START-stop pins

Part Number: TDC1000

Hello,

 I have a doubt regarding interfacing tdc1000 to atmega328. I have given the start/stop output to normal i/o pins of atmega328. I noticed that in schematic, the outptut was given to the interrupt pins of msp. I could still get measurement from atmega, but not frequently i.e., the number of times i get a measurement is less than the number of time i get a timeout error( i have given a timeout error when stop pulse is not read within a given time say about 3000microseconds). Would that be of problem... Or is it something else? . 

In my setup I have glued the trasnducer to a box and made it float on water. A quick reply would be of great help!

Regards,

Shankar