Note that pops and hisses should not be possible on a digital system, and are usually caused by external factors. Pauses are generally caused by data loss on overloaded links.
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Is the call being routed over the Internet, or other WAN link? If so, then you may simply not have enough bandwidth on the link. It may help to configure the link to use low-bandwidth codecs.
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If the problem is occurring on calls made internally, or via an ISDN link, then it is possibly a LAN traffic issue. Try connecting the phone to a switch port that is closer to the PABX and see if that improves the quality. Ensure that the network is switched, and does not use hubs. Use a network monitor to check that there is not a large amount of broadcast traffic on the LAN.