First: why to 9.6.1? Even the 9.6.x code line is out of normal support by now (all 9.x code lines have reached the end of their lifetime), so you should upgrade to 10.2 (less bugs than 10.1.x, as far as I can tell).
Or is this an intermediate upgrade? Then I take back this question.
Second: what version of 9.6.1 did you install on what hardware / OS platform?
What's the repository DBMS in what version, and which DB client did you install to access the repository database(s)?
Is there anything in the domain log which might indicate the cause of trouble?
Since a higher version is not compatible with our Product , we cannot go in for any other version.
Also , It was working perfectly fine with 9.5
We use Oracle 11.2.04 vesrion
Sorry for my curiosity, but what do you mean that a "higher version is not compatible with our product"?
From 9.5 to 9.6 Informatica has applied (again) changes to the low-level network libraries. So it is no wonder that 9.6 causes more network traffic than 9.5. And if this increase in network traffic leads to significantly more network collisions (e.g. on the TCP level), then this would explain the drop-outs you are experiencing.
Please work with your network administrators to analyse the average and top rates of TCP collisions on the affected subnets. It may become necessary / useful to restructure the subnets.