Lync is a complex product. There is a saying among Lync professionals that Lync is not usually the problem, its what lync is dropped into; This underlying environment is usually not set to optimally cater to the needs of real time audio. “That is usually the underlying issue”.
I can tell you this is a true statement. Lync is actually somewhat simple in many ways. Lync does ask the Network to do things it normally is not designed for. Lync is a product that asks more of a network, then any product to come before it.
That said, this puts you at odds with the network group on your deployment. you may need to supply the burden of proof that there is a network problem. I have begun a series of videos on wire shark troubleshooting. They were part of a challenge and I cant supply you with the trace file, but I can show you the videos, which contain the methodology to isolate a TCP latency issue. Please enjoy the 3 Video Play list at:
I hope this may be helpful.