Darwin Streaming Server tweaking

We're running Darwin Streaming Server broadcasting 20hours day. We have a 100mps cap, and are trying to prevent glitchy video. We reconvert everything using menencoder. We never have audio problems but some videos, even though they've all been encoded identically still are problematic at times. I'm not sure if this is an encoding issue, port problem, keyframes, ttl, or how darwin server decides to encode the video sends it out. It most likely is a simple fix but need a DSS expert to have a look.