You have to remember that IP was never designed for time sensitive data transfer such as voice, audio and video. There is nothing in the protocol itself to control latency. Latency can be controlled by routers that are protocol aware and can enforce Quality of Service (QoS), but even then they are limited in what they can do.
The big problem with the co-existence of general purpose data and time sensitive media data on the same network is packet size. Only one packet at a time is every transferred across a link. If a file transfer uses full size (1518 bytes) or jumbo packets (9000 bytes), VoIP packets will have to wait a while until they get their turn at the link. Media devices deal with this by increasing buffer sizes which means greater latency.
If your company's server recently changed settings to allow jumbo packets, that could explain the change in behavior.
Some VoIP products can be installed as a gateway between the home network and the Internet while providing some QoS. If your equipment supports this you should try it. Even then, large packets are a problem as they can't (easily) be broken up.
Good Luck.