Zo,
Have you tried swapping cables between USRP's? both REF/PPS and signal (one at 
a time) to see if the apparent phase differences follow particular 
cables/signal paths?

On Apr 3, 2013, at 2:32 AM, Zooz Engineer <xtmpcvs...@hotmail.com> wrote:

> Hi Marcus, 
> 
> Thanks for replying. I did the following test after your comments: 
> 
> 1- to rule out the scope sink problem, I used a file sink and plotted the 
> output using octave: Same results observed. 
> 2- I took the outputs of the splitters to the oscilloscope and there are 
> aligned. 
> 
> Are there other ways to test Ref/PPS other than the one I mentioned in my 
> original mesage? 
> 
> Best/ 
> 
> Zo
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